.hash.hdr <- "result/step1/hash"
.hash.data <- fileset.list(.hash.hdr)
.hash.info <- read.hash(.hash.data)
.mkdir("result/step5/deg/")

major.deg.tab <- fread("Tab/DEG_MS_vs_HC.txt.gz")

1. mTconv subtype DEG analysis

annot.dt <-
    fread("Tab/step4_mtconv_leiden.txt.gz") %>%
    left_join(.hash.info) %>%
    na.omit()

nnz.cutoff <- 100
cv.cutoff <- 0.8

.data <- fileset.list("result/step1/matrix")
.deg.data <- fileset.list("result/step5/deg/mtconv_hc_ms")

if.needed(.deg.data, {
    .deg.data <-
        rcpp_mmutil_copy_selected_columns(.data$mtx,
                                          .data$row,
                                          .data$col,
                                          unique(annot.dt$tag),
                                          "result/step5/deg/mtconv_hc_ms")
})

.scores <- rcpp_mmutil_compute_scores(.deg.data$mtx,
                                      .deg.data$row,
                                      .deg.data$col)

row.scores <- setDT(.scores$row) %>%
    rename(gene = name) %>%                      # 
    filter(!str_detect(`gene`,"[Hh]ashtag")) %>% # remove hashtag
    as.data.table() %>%
    parse.gene()

Gene-level statistics confirm that some genes are not expressed much

.genes.interest <- c("PRDM1", "SGK1", "LBH", "DDIT4")

.dt.show <- 
    row.scores[hgnc_symbol %in% .genes.interest] %>% 
    arrange(`nnz`) %>% 
    mutate(x = `nnz`, y = 5000 + 100 * (1:n())) %>%
    mutate(lab = hgnc_symbol %&% "\n(" %&% `nnz` %&% ")")

plt <-
    ggplot(row.scores, aes((`nnz`))) +
    theme_classic() + ggtitle("Gene-level statistics: histogram of number of non-zeros") +
    geom_histogram(fill="gray", linewidth=.1, color="gray20", bins=50) +
    ggrepel::geom_text_repel(aes(x, y, label=lab),
                             data=.dt.show,
                             size = 4, color = 2, vjust=0, hjust=0) +
    geom_vline(aes(xintercept = x), data = .dt.show, lty = 2, col = 2) +
    scale_y_log10("count") +
    scale_x_continuous("number of non-zero across " %&% num.int(.scores$max.col) %&% " cells",
                       breaks = c(unique(.dt.show$x), c(0, 5000, 15000, 20000)))
print(plt)

.file <- fig.dir %&% "/Fig_mTconv_gene_scores_nnz.pdf"
.gg.save(filename = .file, plot = plt, width=8, height=3)

PDF

Creating Q/C’ed DEG data

qc.features <- row.scores[nnz > nnz.cutoff & cv > cv.cutoff]

.qc.hdr <- "result/step5/deg/qc_mtconv_hc_ms"
.qc.data <- fileset.list(.qc.hdr)

if.needed(.qc.data, {
    .qc.data <-
        rcpp_mmutil_copy_selected_rows(.deg.data$mtx,
                                       .deg.data$row,
                                       .deg.data$col,
                                       qc.features$gene,
                                       .qc.hdr)
})

.file <- "result/step5/deg/mtconv_hc_ms.rds"

if.needed(.file, {

    .membership <-
        annot.dt[, .(tag, membership)] %>%
        as.data.frame()

    .cell2indv <- annot.dt[, .(tag, subject)] %>%
        unique %>%
        as.data.frame()

    .indv2exp <- .cell2indv %>%
        select(subject) %>%
        mutate(disease = substr(`subject`, 1, 2)) %>%
        as.data.frame()

    .deg.stat <-
        make.cocoa(.qc.data, .membership, .cell2indv, .indv2exp,
                   knn = 100, .rank = 15, .take.ln = TRUE,
                   impute.by.knn = TRUE, num.threads = 16)

   saveRDS(.deg.stat, .file)
})
.deg.stat <- readRDS(.file)

.cts <- unique(annot.dt$membership)
.indvs <- unique(annot.dt$subject)

.hc.ms.dt <-
    list(tot = sort.col(.deg.stat$sum, .cts, .indvs),
         cfa = sort.col(.deg.stat$resid.ln.mu, .cts, .indvs),
         cfa.sd = sort.col(.deg.stat$resid.ln.mu.sd, .cts, .indvs)) %>%
    combine.statistics() %>%
    na.omit() %>%
    as.data.table() %>% 
    (function(x) {
        x[, c("sample", "membership") := tstrsplit(as.character(Var2), split="_")];
        x[, disease := substr(`sample`, 1, 2)];
        x[, gene := as.character(Var1)];
        x
    }) %>% 
    dplyr::select(-Var1, -Var2) %>% 
    as.data.table()

hc.ms.deg <-
    summarize.deg(.hc.ms.dt, tot.cutoff = 5) %>%
    parse.gene() %>%
    as.data.table()

DOWNLOAD: mTconv DEG MS vs HC

Found 817 unique genes strongly perturbed by MS with FDR 10%

Up-regulated: 112
Down-regulated: 715
Total pairs of genes and clusters: 26,066

count.deg <- function(.dt, fdr.cutoff = .1) {
    .dt[fdr < fdr.cutoff &
        sign(ADD) == sign(ADE) &
        sign(ADC) == sign(ADE),
        .(n = .N),
        by = .(membership,
               direction = if_else(z > 0, "up", "down"))
        ] %>%
        mutate(direction = factor(direction, c("up", "down"))) %>%
        group_by(membership) %>%
        arrange(desc(direction)) %>%
        mutate(nc = cumsum(n)) %>%
        ungroup
}

.file <- fig.dir %&% "/Fig_mTconv_DEG_count.pdf"
.gg.save(filename = .file, plot = plt, width=2, height=2)

PDF

Examples

hc.ms.deg[, c("ensembl_gene_id", "hgnc_symbol") := tstrsplit(`gene`, split="_")]

major.deg <- major.deg.tab[fwer < .05]$hgnc_symbol

.genes.show <-
    hc.ms.deg[hgnc_symbol %in% major.deg &
              sign(ADD) == sign(ADE) &
              sign(ADC) == sign(ADE)] %>%
    select(gene) %>%
    unique() %>%
    unlist() %>%
    as.character()

ensembl_gene_id	hgnc_symbol	z_1	z_2	z_3	pv_1	pv_2	pv_3	fdr_1	fdr_2	fdr_3	.link
	CD127	11.29	-8.09	1.73	1.4e-29	5.97e-16	8.42e-02	1.51e-26	2.47e-13	6.38e-01	PDF
	CD137	-3.43	-4.57	-5.24	6.08e-04	4.97e-06	1.6e-07	5.93e-02	4.69e-04	3.66e-05	PDF
	CD161	0.26	-7.25	-4.25	7.94e-01	4.16e-13	2.16e-05	1e+00	1.45e-10	2.84e-03	PDF
	CD184	-2.73	-0.63	4.69	6.27e-03	5.28e-01	2.71e-06	2.79e-01	7.98e-01	4.91e-04	PDF
	CD185	6.74	2.89	-2.12	1.62e-11	3.86e-03	3.37e-02	6.68e-09	6.42e-02	4.62e-01	PDF
	CD19	1.94	0.34	-0.73	5.21e-02	7.31e-01	4.68e-01	7.06e-01	9.04e-01	9.26e-01	PDF
	CD20	-14.93	-12.09	-13.6	1.97e-50	1.17e-33	4.19e-42	3.41e-47	1.27e-30	4.05e-39	PDF
	CD226	14.5	8.31	-1.09	1.15e-47	9.25e-17	2.75e-01	1.66e-44	4.23e-14	8.52e-01	PDF
	CD25	-4.63	-16.19	7.89	3.67e-06	6.25e-59	3.05e-15	8.38e-04	1.36e-55	1.56e-12	PDF
	CD27	-33.42	-60.54	-20.85	7.88e-245	0e+00	1.61e-96	3.41e-241	0e+00	2.33e-93	PDF
	CD278	17.15	8.24	16.38	6.43e-66	1.7e-16	2.65e-60	1.86e-62	7.41e-14	2.89e-57	PDF
	CD279	7.72	8.37	-3.08	1.2e-14	5.84e-17	2.07e-03	6.91e-12	2.82e-14	1.03e-01	PDF
	CD3	2.7	-9.67	-37.25	6.96e-03	3.95e-22	1.16e-303	2.96e-01	2.14e-19	5.03e-300	PDF
	CD366	-0.28	2.49	-0.71	7.8e-01	1.26e-02	4.79e-01	1e+00	1.28e-01	9.3e-01	PDF
	CD45RA	-65.64	-75.92	-26.48	0e+00	0e+00	1.56e-154	0e+00	0e+00	2.71e-151	PDF
	CD8a	-4.59	-1.17	0.03	4.49e-06	2.42e-01	9.76e-01	9.49e-04	5.75e-01	1e+00	PDF
ENSG00000003056	M6PR	-0.62	-1.75	-0.85	5.35e-01	8.06e-02	3.96e-01	1e+00	3.38e-01	9.08e-01	PDF
ENSG00000008988	RPS20	-1.54	-2.89	-1.96	1.23e-01	3.89e-03	5e-02	8.87e-01	6.45e-02	5.32e-01	PDF
ENSG00000009790	TRAF3IP3	-2.09	-5.41	-4.35	3.65e-02	6.19e-08	1.34e-05	6.31e-01	1.01e-05	1.85e-03	PDF
ENSG00000009844	VTA1	-2.78	-4.63	-1.51	5.48e-03	3.71e-06	1.31e-01	2.6e-01	3.56e-04	7.2e-01	PDF
ENSG00000013573	DDX11	-0.03	-0.88	-2.72	9.75e-01	3.8e-01	6.52e-03	1e+00	7.05e-01	2.01e-01	PDF
ENSG00000019582	CD74	-0.32	-2.06	-2.29	7.49e-01	3.98e-02	2.2e-02	1e+00	2.38e-01	3.88e-01	PDF
ENSG00000025708	TYMP	0.76	-1.35	1.4	4.45e-01	1.77e-01	1.61e-01	1e+00	4.92e-01	7.61e-01	PDF
ENSG00000026297	RNASET2	0.94	-0.43	-0.52	3.46e-01	6.67e-01	6.01e-01	1e+00	8.73e-01	9.61e-01	PDF
ENSG00000026508	CD44	0.73	1.29	-0.93	4.65e-01	1.97e-01	3.5e-01	1e+00	5.18e-01	8.92e-01	PDF
ENSG00000030582	GRN	0.15	-1.75	-0.19	8.81e-01	8.01e-02	8.47e-01	1e+00	3.37e-01	9.96e-01	PDF
ENSG00000036448	MYOM2	0.98	-1.34	6.46	3.27e-01	1.8e-01	1.02e-10	1e+00	4.97e-01	4.24e-08	PDF
ENSG00000038274	MAT2B	-0.78	-3.59	-0.79	4.37e-01	3.29e-04	4.32e-01	1e+00	1.18e-02	9.2e-01	PDF
ENSG00000041357	PSMA4	-1.97	-4.48	-2.91	4.84e-02	7.46e-06	3.65e-03	6.93e-01	6.42e-04	1.47e-01	PDF
ENSG00000047410	TPR	-2.5	-1.51	-3.78	1.23e-02	1.31e-01	1.54e-04	3.94e-01	4.28e-01	1.57e-02	PDF
ENSG00000048405	ZNF800	-1.67	-1.37	0.39	9.53e-02	1.69e-01	6.95e-01	8.25e-01	4.81e-01	9.79e-01	PDF
ENSG00000051108	HERPUD1	4.08	4.22	4.19	4.44e-05	2.44e-05	2.77e-05	7e-03	1.64e-03	3.6e-03	PDF
ENSG00000057657	PRDM1	2.18	1.15	3.49	2.96e-02	2.51e-01	4.86e-04	5.78e-01	5.84e-01	3.95e-02	PDF
ENSG00000059377	TBXAS1	0.29	-0.43	1.18	7.73e-01	6.66e-01	2.37e-01	1e+00	8.72e-01	8.35e-01	PDF
ENSG00000059804	SLC2A3	0.98	-0.87	-0.56	3.28e-01	3.82e-01	5.75e-01	1e+00	7.06e-01	9.56e-01	PDF
ENSG00000064933	PMS1	-0.57	-1.65	-3.01	5.69e-01	9.9e-02	2.63e-03	1e+00	3.73e-01	1.21e-01	PDF
ENSG00000066379	ZNRD1	-1.69	-1.54	-1.2	9.16e-02	1.25e-01	2.3e-01	8.23e-01	4.17e-01	8.3e-01	PDF
ENSG00000067082	KLF6	-4.37	-5.49	-2	1.25e-05	4.02e-08	4.53e-02	2.2e-03	7.27e-06	5.11e-01	PDF
ENSG00000069399	BCL3	0.18	3.62	2.55	8.55e-01	2.96e-04	1.06e-02	1e+00	1.11e-02	2.67e-01	PDF
ENSG00000069424	KCNAB2	-5.3	-3.62	-0.76	1.15e-07	2.98e-04	4.48e-01	3.43e-05	1.11e-02	9.26e-01	PDF
ENSG00000069493	CLEC2D	-1.51	-3.34	-3.57	1.3e-01	8.38e-04	3.51e-04	8.99e-01	2.36e-02	3.02e-02	PDF
ENSG00000071073	MGAT4A	0.07	4.06	2.71	9.43e-01	4.86e-05	6.69e-03	1e+00	2.91e-03	2.03e-01	PDF
ENSG00000073578	SDHA	-1.36	-1.04	-1.38	1.75e-01	2.99e-01	1.67e-01	9.66e-01	6.29e-01	7.73e-01	PDF
ENSG00000077420	APBB1IP	-1.16	-4.38	-1.9	2.47e-01	1.2e-05	5.8e-02	1e+00	9.35e-04	5.51e-01	PDF
ENSG00000078304	PPP2R5C	0.37	-1.49	-2.09	7.09e-01	1.37e-01	3.7e-02	1e+00	4.37e-01	4.69e-01	PDF
ENSG00000081059	TCF7	-1.91	-4.43	-1.7	5.57e-02	9.47e-06	8.91e-02	7.15e-01	7.76e-04	6.49e-01	PDF
ENSG00000083223	TUT7	-2.01	-4.46	-1.94	4.48e-02	8.38e-06	5.29e-02	6.88e-01	6.95e-04	5.38e-01	PDF
ENSG00000087074	PPP1R15A	-1.61	-2.49	-4.54	1.07e-01	1.28e-02	5.62e-06	8.46e-01	1.3e-01	9.06e-04	PDF
ENSG00000088986	DYNLL1	-1.18	-4.71	-3.57	2.37e-01	2.46e-06	3.5e-04	1e+00	2.48e-04	3.02e-02	PDF
ENSG00000089692	LAG3	0.47	0.26	0.75	6.37e-01	7.91e-01	4.52e-01	1e+00	9.33e-01	9.26e-01	PDF
ENSG00000090104	RGS1	-2.35	-3.26	-1.81	1.88e-02	1.1e-03	6.99e-02	4.89e-01	2.81e-02	5.92e-01	PDF
ENSG00000091317	CMTM6	1.36	-0.72	6.2	1.72e-01	4.7e-01	5.58e-10	9.65e-01	7.63e-01	1.87e-07	PDF
ENSG00000092820	EZR	-0.38	0.47	0.17	7.01e-01	6.38e-01	8.64e-01	1e+00	8.54e-01	9.96e-01	PDF
ENSG00000099985	OSM	3.75	0.72	4.46	1.8e-04	4.71e-01	8.29e-06	2.26e-02	7.64e-01	1.22e-03	PDF
ENSG00000100097	LGALS1	5.88	4.37	6.03	4.13e-09	1.27e-05	1.63e-09	1.33e-06	9.73e-04	4.74e-07	PDF
ENSG00000100201	DDX17	0.12	-3.29	-3.2	9.01e-01	1.01e-03	1.39e-03	1e+00	2.66e-02	8.21e-02	PDF
ENSG00000100219	XBP1	2.25	0.35	3.78	2.43e-02	7.26e-01	1.58e-04	5.54e-01	9.02e-01	1.57e-02	PDF
ENSG00000100288	CHKB	-0.67	-0.64	-0.22	5.02e-01	5.22e-01	8.24e-01	1e+00	7.95e-01	9.91e-01	PDF
ENSG00000100300	TSPO	1.71	1.52	4.05	8.79e-02	1.28e-01	5.02e-05	8.11e-01	4.23e-01	6.24e-03	PDF
ENSG00000100906	NFKBIA	7.6	6.39	12.4	3.06e-14	1.62e-10	2.52e-35	1.66e-11	4.85e-08	2.19e-32	PDF
ENSG00000101439	CST3	0.55	-1.24	0.49	5.82e-01	2.16e-01	6.25e-01	1e+00	5.42e-01	9.63e-01	PDF
ENSG00000101695	RNF125	0.37	1.5	0.26	7.08e-01	1.34e-01	7.91e-01	1e+00	4.32e-01	9.87e-01	PDF
ENSG00000102007	PLP2	1.47	-0.14	3.55	1.42e-01	8.9e-01	3.88e-04	9.26e-01	9.67e-01	3.28e-02	PDF
ENSG00000102109	PCSK1N	0.36	1.08	2.66	7.16e-01	2.82e-01	7.85e-03	1e+00	6.14e-01	2.25e-01	PDF
ENSG00000102226	USP11	-2.51	-2.93	-2.17	1.22e-02	3.44e-03	2.98e-02	3.94e-01	5.97e-02	4.38e-01	PDF
ENSG00000102245	CD40LG	-1.12	-4.41	-1.58	2.63e-01	1.05e-05	1.14e-01	1e+00	8.43e-04	6.99e-01	PDF
ENSG00000102760	RGCC	0.08	-5.1	-2.38	9.38e-01	3.37e-07	1.75e-02	1e+00	4.66e-05	3.49e-01	PDF
ENSG00000103064	SLC7A6	-2.87	-2.29	-1.51	4.07e-03	2.21e-02	1.32e-01	2.09e-01	1.71e-01	7.2e-01	PDF
ENSG00000103121	CMC2	0.4	-0.2	-1.76	6.86e-01	8.44e-01	7.82e-02	1e+00	9.52e-01	6.18e-01	PDF
ENSG00000103202	NME4	-0.55	-0.13	0.95	5.85e-01	8.98e-01	3.4e-01	1e+00	9.7e-01	8.84e-01	PDF
ENSG00000103479	RBL2	-0.53	-1.34	-0.43	5.98e-01	1.81e-01	6.67e-01	1e+00	4.98e-01	9.75e-01	PDF
ENSG00000103811	CTSH	1	-1.08	3.48	3.16e-01	2.79e-01	4.93e-04	1e+00	6.12e-01	3.97e-02	PDF
ENSG00000105655	ISYNA1	-0.88	-0.84	-2.35	3.78e-01	4.03e-01	1.87e-02	1e+00	7.22e-01	3.61e-01	PDF
ENSG00000105835	NAMPT	-1.15	-0.8	-1.28	2.51e-01	4.26e-01	2e-01	1e+00	7.37e-01	8.08e-01	PDF
ENSG00000106460	TMEM106B	-0.61	-2.11	-0.51	5.4e-01	3.51e-02	6.12e-01	1e+00	2.22e-01	9.62e-01	PDF
ENSG00000106560	GIMAP2	-2.97	-1.2	-2.58	2.94e-03	2.3e-01	1e-02	1.72e-01	5.62e-01	2.55e-01	PDF
ENSG00000106605	BLVRA	0.93	-2.33	-0.07	3.55e-01	1.98e-02	9.46e-01	1e+00	1.62e-01	9.99e-01	PDF
ENSG00000107281	NPDC1	-3.14	2.84	0.68	1.7e-03	4.5e-03	5e-01	1.22e-01	7.09e-02	9.36e-01	PDF
ENSG00000107738	VSIR	0.15	0.51	0.84	8.78e-01	6.12e-01	4.01e-01	1e+00	8.43e-01	9.12e-01	PDF
ENSG00000107968	MAP3K8	0.2	-1.84	-0.54	8.45e-01	6.61e-02	5.89e-01	1e+00	3.07e-01	9.58e-01	PDF
ENSG00000108590	MED31	0.21	-1.57	-2.37	8.37e-01	1.16e-01	1.76e-02	1e+00	4.04e-01	3.51e-01	PDF
ENSG00000108622	ICAM2	-1.94	-6.14	-4.01	5.18e-02	8.09e-10	6.16e-05	7.06e-01	2.13e-07	7.34e-03	PDF
ENSG00000109775	UFSP2	-0.65	-1.15	-1.6	5.13e-01	2.52e-01	1.09e-01	1e+00	5.85e-01	6.91e-01	PDF
ENSG00000110172	CHORDC1	0.7	-1.62	-0.46	4.82e-01	1.04e-01	6.44e-01	1e+00	3.81e-01	9.68e-01	PDF
ENSG00000110848	CD69	-3.1	-3.28	-0.66	1.95e-03	1.03e-03	5.1e-01	1.35e-01	2.68e-02	9.39e-01	PDF
ENSG00000111679	PTPN6	-0.17	-5.01	-1.81	8.66e-01	5.52e-07	6.96e-02	1e+00	6.86e-05	5.91e-01	PDF
ENSG00000111796	KLRB1	-0.51	-3.94	3.03	6.14e-01	8.11e-05	2.44e-03	1e+00	4.3e-03	1.15e-01	PDF
ENSG00000112110	MRPL18	-3.52	-4.2	-2.61	4.31e-04	2.63e-05	9.01e-03	4.5e-02	1.76e-03	2.4e-01	PDF
ENSG00000112486	CCR6	0.35	0.52	1.31	7.29e-01	6.03e-01	1.89e-01	1e+00	8.38e-01	7.98e-01	PDF
ENSG00000112773	TENT5A	0.23	0.62	0.34	8.16e-01	5.34e-01	7.35e-01	1e+00	8.01e-01	9.82e-01	PDF
ENSG00000113088	GZMK	-8.16	-2.73	-0.14	3.25e-16	6.28e-03	8.9e-01	2.01e-13	8.72e-02	9.98e-01	PDF
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ENSG00000198502	HLA-DRB5	0	-1.06	-1.65	1e+00	2.89e-01	9.81e-02	1e+00	6.21e-01	6.69e-01	PDF
ENSG00000198771	RCSD1	-0.75	-2.15	-2.09	4.51e-01	3.17e-02	3.63e-02	1e+00	2.08e-01	4.67e-01	PDF
ENSG00000198805	PNP	-1.3	-4.46	-1.92	1.94e-01	8.13e-06	5.51e-02	9.86e-01	6.93e-04	5.42e-01	PDF
ENSG00000198830	HMGN2	1.53	-1.87	-0.07	1.25e-01	6.11e-02	9.47e-01	8.91e-01	2.95e-01	9.99e-01	PDF
ENSG00000204161	TMEM273	-3.59	0	-2.24	3.32e-04	9.97e-01	2.49e-02	3.78e-02	1e+00	4.03e-01	PDF
ENSG00000204261	PSMB8-AS1	-2.26	-3.2	-2.08	2.36e-02	1.37e-03	3.77e-02	5.52e-01	3.29e-02	4.7e-01	PDF
ENSG00000204389	HSPA1A	-3.14	-2.37	-0.81	1.68e-03	1.78e-02	4.19e-01	1.22e-01	1.55e-01	9.15e-01	PDF
ENSG00000204472	AIF1	-2.38	-3.9	-1.5	1.71e-02	9.7e-05	1.33e-01	4.65e-01	4.93e-03	7.21e-01	PDF
ENSG00000204677	FAM153C	0	-0.87	-1.36	1e+00	3.87e-01	1.75e-01	1e+00	7.09e-01	7.86e-01	PDF
ENSG00000205138	SDHAF1	0.04	-1.72	-0.35	9.67e-01	8.55e-02	7.27e-01	1e+00	3.49e-01	9.82e-01	PDF
ENSG00000205268	PDE7A	-1.46	0.02	-2.98	1.43e-01	9.83e-01	2.89e-03	9.26e-01	9.98e-01	1.27e-01	PDF
ENSG00000205707	ETFRF1	-2.51	-2.1	-0.11	1.2e-02	3.54e-02	9.12e-01	3.94e-01	2.23e-01	9.98e-01	PDF
ENSG00000211694	TRGV10	0.2	0.03	1.22	8.39e-01	9.77e-01	2.23e-01	1e+00	9.97e-01	8.27e-01	PDF
ENSG00000211706	TRBV6-1	3.93	-7.46	1.65	8.51e-05	8.33e-14	9.84e-02	1.23e-02	3.15e-11	6.69e-01	PDF
ENSG00000211710	TRBV4-1	6.56	1.92	3.03	5.48e-11	5.51e-02	2.48e-03	2.16e-08	2.81e-01	1.15e-01	PDF
ENSG00000211716	TRBV9	2.75	-2.3	12.18	5.91e-03	2.13e-02	4.17e-34	2.67e-01	1.67e-01	3.3e-31	PDF
ENSG00000211721	TRBV6-5	0.53	0.75	3.59	5.95e-01	4.55e-01	3.31e-04	1e+00	7.54e-01	2.95e-02	PDF
ENSG00000211724	TRBV6-6	-2.89	-0.83	-4.55	3.87e-03	4.07e-01	5.31e-06	2.03e-01	7.24e-01	8.89e-04	PDF
ENSG00000211727	TRBV7-6	-0.05	-1.88	2.66	9.63e-01	5.97e-02	7.79e-03	1e+00	2.91e-01	2.25e-01	PDF
ENSG00000211734	TRBV5-1	0.54	4.9	-5.38	5.88e-01	9.68e-07	7.52e-08	1e+00	1.12e-04	1.87e-05	PDF
ENSG00000211745	TRBV4-2	-4.73	-10.49	-4.93	2.23e-06	9.35e-26	8.39e-07	5.69e-04	6.77e-23	1.59e-04	PDF
ENSG00000211747	TRBV20-1	1.49	-3.13	-2.87	1.37e-01	1.74e-03	4.05e-03	9.2e-01	3.8e-02	1.54e-01	PDF
ENSG00000211751	TRBC1	-4.43	-1.7	-2.15	9.31e-06	8.97e-02	3.13e-02	1.75e-03	3.57e-01	4.48e-01	PDF
ENSG00000211753	TRBV28	4.72	2.28	5.29	2.34e-06	2.29e-02	1.21e-07	5.79e-04	1.74e-01	2.92e-05	PDF
ENSG00000211779	TRAV5	0.86	-0.21	3.61	3.9e-01	8.37e-01	3.02e-04	1e+00	9.48e-01	2.79e-02	PDF
ENSG00000211780	TRAV6	-1.1	-1.88	0.59	2.69e-01	5.95e-02	5.53e-01	1e+00	2.9e-01	9.5e-01	PDF
ENSG00000211782	TRAV8-1	-0.98	-2.81	3.05	3.26e-01	4.93e-03	2.26e-03	1e+00	7.48e-02	1.11e-01	PDF
ENSG00000211786	TRAV8-2	-2.61	-5	-3.19	9.01e-03	5.86e-07	1.42e-03	3.44e-01	7.18e-05	8.27e-02	PDF
ENSG00000211788	TRAV13-1	-1.56	-5.47	-3.03	1.2e-01	4.47e-08	2.41e-03	8.83e-01	7.77e-06	1.15e-01	PDF
ENSG00000211789	TRAV12-2	-0.42	3.09	-1.26	6.74e-01	2.01e-03	2.08e-01	1e+00	4.2e-02	8.12e-01	PDF
ENSG00000211790	TRAV8-4	1.17	2.39	3.57	2.41e-01	1.67e-02	3.55e-04	1e+00	1.5e-01	3.03e-02	PDF
ENSG00000211794	TRAV12-3	0.26	-2.09	4.97	7.94e-01	3.64e-02	6.53e-07	1e+00	2.26e-01	1.26e-04	PDF
ENSG00000211795	TRAV8-6	-0.19	-0.47	-6.31	8.52e-01	6.4e-01	2.81e-10	1e+00	8.56e-01	1.06e-07	PDF
ENSG00000211796	TRAV16	0	-4.41	-3.66	9.98e-01	1.03e-05	2.53e-04	1e+00	8.4e-04	2.42e-02	PDF
ENSG00000211801	TRAV21	-3.42	-1.75	-5.27	6.27e-04	7.95e-02	1.35e-07	5.97e-02	3.37e-01	3.19e-05	PDF
ENSG00000211809	TRAV27	-4.34	2.46	-2.14	1.43e-05	1.37e-02	3.2e-02	2.48e-03	1.35e-01	4.52e-01	PDF
ENSG00000211810	TRAV29DV5	-4.06	-3.37	-7.86	4.84e-05	7.53e-04	3.92e-15	7.49e-03	2.2e-02	1.9e-12	PDF
ENSG00000211812	TRAV26-2	2.38	-1.99	-1.03	1.74e-02	4.69e-02	3.05e-01	4.66e-01	2.59e-01	8.75e-01	PDF
ENSG00000211817	TRAV38-2DV8	-5.12	-2.44	-2.16	3.11e-07	1.49e-02	3.06e-02	9e-05	1.42e-01	4.42e-01	PDF
ENSG00000211820	TRAV41	-1.44	-5.82	-1.69	1.49e-01	5.93e-09	9.03e-02	9.32e-01	1.23e-06	6.52e-01	PDF
ENSG00000213145	CRIP1	1.3	0.38	2.38	1.95e-01	7.03e-01	1.73e-02	9.87e-01	8.91e-01	3.49e-01	PDF
ENSG00000213203	GIMAP1	-1.24	-2.96	-1.94	2.15e-01	3.04e-03	5.27e-02	1e+00	5.48e-02	5.38e-01	PDF
ENSG00000213402	PTPRCAP	-0.34	-1.58	1.51	7.3e-01	1.14e-01	1.32e-01	1e+00	4.01e-01	7.2e-01	PDF
ENSG00000213626	LBH	-4.4	-3.14	-2.97	1.06e-05	1.67e-03	3e-03	1.92e-03	3.7e-02	1.29e-01	PDF
ENSG00000215845	TSTD1	-1.63	-1.67	-2.41	1.03e-01	9.42e-02	1.62e-02	8.39e-01	3.63e-01	3.43e-01	PDF
ENSG00000226067	LINC00623	-1.68	-3.12	-3.25	9.24e-02	1.82e-03	1.16e-03	8.23e-01	3.9e-02	7.32e-02	PDF
ENSG00000226660	TRBV2	-0.28	-5.35	-2.32	7.78e-01	8.78e-08	2.01e-02	1e+00	1.39e-05	3.74e-01	PDF
ENSG00000230099	TRBV5-4	-2	-6.12	-4.57	4.56e-02	9.26e-10	4.98e-06	6.89e-01	2.3e-07	8.67e-04	PDF
ENSG00000231682	LINC01891	NaN	-1.06	0	Inf	2.91e-01	1e+00	Inf	6.23e-01	1e+00	PDF
ENSG00000232869	TRBV29-1	2.47	6.42	-0.3	1.36e-02	1.33e-10	7.63e-01	4.11e-01	4.14e-08	9.86e-01	PDF
ENSG00000235532	LINC00402	-2.4	-2.95	-1.46	1.66e-02	3.19e-03	1.45e-01	4.55e-01	5.61e-02	7.46e-01	PDF
ENSG00000237702	TRBV3-1	-2.12	3.39	-1.59	3.4e-02	6.95e-04	1.11e-01	6.21e-01	2.09e-02	6.98e-01	PDF
ENSG00000240065	PSMB9	-0.2	-0.76	-1.5	8.38e-01	4.46e-01	1.33e-01	1e+00	7.48e-01	7.21e-01	PDF
ENSG00000241343	RPL36A	1.49	-0.06	0.02	1.37e-01	9.52e-01	9.86e-01	9.2e-01	9.91e-01	1e+00	PDF
ENSG00000241657	TRBV11-2	-5.54	-2.81	-7.17	3.09e-08	4.98e-03	7.46e-13	9.56e-06	7.51e-02	3.24e-10	PDF
ENSG00000242086	MUC20-OT1	-2.71	-1.37	-2.37	6.65e-03	1.7e-01	1.78e-02	2.89e-01	4.82e-01	3.52e-01	PDF
ENSG00000243749	TMEM35B	-3.49	-4.29	-0.11	4.74e-04	1.79e-05	9.12e-01	4.9e-02	1.3e-03	9.98e-01	PDF
ENSG00000243927	MRPS6	-2.06	-4.85	-3.1	3.98e-02	1.23e-06	1.93e-03	6.59e-01	1.35e-04	9.74e-02	PDF
ENSG00000244734	HBB	-0.07	-1.03	-33.41	9.44e-01	3.02e-01	9.64e-245	1e+00	6.31e-01	2.8e-241	PDF
ENSG00000245532	NEAT1	-0.81	-3.15	-2.06	4.2e-01	1.61e-03	3.91e-02	1e+00	3.61e-02	4.77e-01	PDF
ENSG00000245904	AC025164.1	-0.73	-1.45	-1.85	4.68e-01	1.48e-01	6.5e-02	1e+00	4.52e-01	5.76e-01	PDF
ENSG00000246223	LINC01550	-1.61	-0.56	-1.27	1.08e-01	5.76e-01	2.04e-01	8.47e-01	8.26e-01	8.1e-01	PDF
ENSG00000250303	AP002884.1	1.81	0.79	2.8	7.09e-02	4.3e-01	5.08e-03	7.65e-01	7.39e-01	1.76e-01	PDF
ENSG00000253738	OTUD6B-AS1	-2.1	-2.32	-1.45	3.6e-02	2.01e-02	1.48e-01	6.28e-01	1.63e-01	7.47e-01	PDF
ENSG00000254999	BRK1	-0.26	-0.8	-1.47	7.95e-01	4.26e-01	1.41e-01	1e+00	7.37e-01	7.37e-01	PDF
ENSG00000260708	AL118516.1	-0.4	2.61	1.48	6.93e-01	9.09e-03	1.38e-01	1e+00	1.08e-01	7.29e-01	PDF
ENSG00000266338	NBPF15	-0.56	-2.4	-1.39	5.73e-01	1.66e-02	1.63e-01	1e+00	1.5e-01	7.67e-01	PDF
ENSG00000268027	AC243960.1	-1.2	-3.04	-2.51	2.3e-01	2.4e-03	1.22e-02	1e+00	4.75e-02	2.89e-01	PDF
ENSG00000269028	MTRNR2L12	-1.33	-11.82	-7.92	1.85e-01	3.14e-32	2.4e-15	9.82e-01	3.03e-29	1.31e-12	PDF
ENSG00000271109	AC008555.5	-2.21	-3.52	-2.73	2.74e-02	4.38e-04	6.33e-03	5.65e-01	1.48e-02	1.99e-01	PDF
ENSG00000271503	CCL5	-1.02	-2.6	-2.5	3.06e-01	9.3e-03	1.23e-02	1e+00	1.09e-01	2.91e-01	PDF
ENSG00000275074	NUDT18	-0.75	-2.83	1.38	4.52e-01	4.71e-03	1.67e-01	1e+00	7.3e-02	7.73e-01	PDF
ENSG00000275791	TRBV10-3	-1.81	-18.8	0.76	6.97e-02	7.66e-79	4.47e-01	7.63e-01	2.22e-75	9.26e-01	PDF
ENSG00000276557	TRBV18	1.52	2.36	-5.64	1.28e-01	1.82e-02	1.66e-08	8.95e-01	1.56e-01	4.39e-06	PDF
ENSG00000276953	TRBV12-4	-6.03	-2.63	-6.06	1.67e-09	8.53e-03	1.39e-09	5.8e-07	1.04e-01	4.31e-07	PDF
ENSG00000277734	TRAC	-2.76	-4.85	-2.68	5.77e-03	1.22e-06	7.42e-03	2.65e-01	1.35e-04	2.18e-01	PDF
ENSG00000278030	TRBV7-9	-2.95	-4.66	2.48	3.21e-03	3.15e-06	1.31e-02	1.8e-01	3.11e-04	3e-01	PDF
ENSG00000280721	LINC01943	2.29	-0.19	1.24	2.18e-02	8.51e-01	2.14e-01	5.26e-01	9.55e-01	8.18e-01	PDF
ENSG00000282939	TRBV7-2	-8.89	-4.4	-4.39	6.32e-19	1.09e-05	1.14e-05	4.98e-16	8.63e-04	1.62e-03	PDF
ENSG00000283063	TRBV6-2	0.7	-0.22	-0.08	4.85e-01	8.24e-01	9.34e-01	1e+00	9.44e-01	9.99e-01	PDF
ENSG00000283782	AC116366.3	-0.49	-2.78	-0.4	6.23e-01	5.52e-03	6.86e-01	1e+00	8.07e-02	9.78e-01	PDF
ENSG00000285437	POLR2J3	-0.77	-1.14	-0.27	4.43e-01	2.53e-01	7.84e-01	1e+00	5.86e-01	9.87e-01	PDF
	HLA-DR	-4.6	-4.63	-20.05	4.21e-06	3.72e-06	2.19e-89	9.27e-04	3.56e-04	2.72e-86	PDF
	TCRab	1.76	-10.14	-3.48	7.78e-02	3.56e-24	5.05e-04	7.86e-01	2.06e-21	4.03e-02	PDF
	TIGIT	2.19	1.3	-1.64	2.87e-02	1.92e-01	1.02e-01	5.71e-01	5.13e-01	6.74e-01	PDF

Additional genes/proteins

ensembl_gene_id	hgnc_symbol	z_1	z_2	z_3	pv_1	pv_2	pv_3	fdr_1	fdr_2	fdr_3	.link
	CD279	7.72	8.37	-3.08	1.2e-14	5.84e-17	2.07e-03	6.91e-12	2.82e-14	1.03e-01	PDF
	CD366	-0.28	2.49	-0.71	7.8e-01	1.26e-02	4.79e-01	1e+00	1.28e-01	9.3e-01	PDF
ENSG00000049768	FOXP3	0.03	-2.31	0.98	9.78e-01	2.07e-02	3.26e-01	1e+00	1.65e-01	8.82e-01	PDF
ENSG00000089692	LAG3	0.47	0.26	0.75	6.37e-01	7.91e-01	4.52e-01	1e+00	9.33e-01	9.26e-01	PDF
ENSG00000118515	SGK1	0.45	0.53	3.01	6.49e-01	5.94e-01	2.64e-03	1e+00	8.33e-01	1.21e-01	PDF
ENSG00000188389	PDCD1	0.69	2.5	1.75	4.91e-01	1.23e-02	7.95e-02	1e+00	1.26e-01	6.24e-01	PDF
ENSG00000198846	TOX	-0.66	0.63	2.1	5.12e-01	5.31e-01	3.62e-02	1e+00	7.99e-01	4.67e-01	PDF

2. mTreg subtype DEG analysis

annot.dt <-
    fread("Tab/step4_mtreg_leiden.txt.gz") %>%
    left_join(.hash.info) %>%
    na.omit()

.mkdir("result/step5/deg/")
.data <- fileset.list("result/step1/matrix")
.deg.data <- fileset.list("result/step5/deg/mtreg_hc_ms")
.mkdir(dirname(.deg.data$mtx))

if.needed(.deg.data, {
    .deg.data <-
        rcpp_mmutil_copy_selected_columns(.data$mtx,
                                          .data$row,
                                          .data$col,
                                          unique(annot.dt$tag),
                                          "result/step5/deg/mtreg_hc_ms")
})

.scores <- rcpp_mmutil_compute_scores(.deg.data$mtx,
                                      .deg.data$row,
                                      .deg.data$col)

row.scores <- setDT(.scores$row) %>%
    rename(gene = name) %>%                      # 
    filter(!str_detect(`gene`,"[Hh]ashtag")) %>% # remove hashtag
    as.data.table() %>%
    parse.gene()

Gene-level statistics confirm that some genes are not expressed much

.genes.interest <- c("PRDM1", "SGK1", "LBH", "DDIT4")

.dt.show <- 
    row.scores[hgnc_symbol %in% .genes.interest] %>% 
    arrange(`nnz`) %>% 
    mutate(x = `nnz`, y = 5000 + 100 * (1:n())) %>%
    mutate(lab = hgnc_symbol %&% "\n(" %&% `nnz` %&% ")")

plt <-
    ggplot(row.scores, aes((`nnz`))) +
    theme_classic() + ggtitle("Gene-level statistics: histogram of number of non-zeros") +
    geom_histogram(fill="gray", linewidth=.1, color="gray20", bins=50) +
    ggrepel::geom_text_repel(aes(x, y, label=lab),
                             data=.dt.show,
                             size = 4, color = 2, vjust=0, hjust=0) +
    geom_vline(aes(xintercept = x), data = .dt.show, lty = 2, col = 2) +
    scale_y_log10("count") +
    scale_x_continuous("number of non-zero across " %&% num.int(.scores$max.col) %&% " cells",
                       breaks = c(unique(.dt.show$x), c(0, 5000, 15000, 20000)))
print(plt)

.file <- fig.dir %&% "/Fig_mTreg_gene_scores_nnz.pdf"
.gg.save(filename = .file, plot = plt, width=8, height=3)

PDF

Creating Q/C’ed DEG data

qc.features <- row.scores[nnz > nnz.cutoff & cv > cv.cutoff]

.qc.hdr <- "result/step5/deg/qc_mtreg_hc_ms"
.qc.data <- fileset.list(.qc.hdr)

if.needed(.qc.data, {
    .qc.data <-
        rcpp_mmutil_copy_selected_rows(.deg.data$mtx,
                                       .deg.data$row,
                                       .deg.data$col,
                                       qc.features$gene,
                                       .qc.hdr)
})

.file <- "result/step5/deg/mtreg_hc_ms.rds"

if.needed(.file, {

    .membership <-
        annot.dt[, .(tag, membership)] %>%
        as.data.frame()

    .cell2indv <- annot.dt[, .(tag, subject)] %>%
        unique %>%
        as.data.frame()

    .indv2exp <- .cell2indv %>%
        select(subject) %>%
        mutate(disease = substr(`subject`, 1, 2)) %>%
        as.data.frame()

    .deg.stat <-
        make.cocoa(.qc.data, .membership, .cell2indv, .indv2exp,
                   knn = 100, .rank = 15, .take.ln = TRUE,
                   impute.by.knn = TRUE, num.threads = 16)

   saveRDS(.deg.stat, .file)
})
.deg.stat <- readRDS(.file)

.cts <- unique(annot.dt$membership)
.indvs <- unique(annot.dt$subject)

.hc.ms.dt <-
    list(tot = sort.col(.deg.stat$sum, .cts, .indvs),
         cfa = sort.col(.deg.stat$resid.ln.mu, .cts, .indvs),
         cfa.sd = sort.col(.deg.stat$resid.ln.mu.sd, .cts, .indvs)) %>%
    combine.statistics() %>%
    na.omit() %>%
    as.data.table() %>% 
    (function(x) {
        x[, c("sample", "membership") := tstrsplit(as.character(Var2), split="_")];
        x[, disease := substr(`sample`, 1, 2)];
        x[, gene := as.character(Var1)];
        x
    }) %>% 
    dplyr::select(-Var1, -Var2) %>% 
    as.data.table()

hc.ms.deg <-
    summarize.deg(.hc.ms.dt, tot.cutoff = 5) %>%
    parse.gene()

DOWNLOAD: mtreg DEG MS vs HC

Found 1,703 unique genes strongly perturbed by MS with FDR 10%

Up-regulated: 221
Down-regulated: 1,512
Total pairs of genes and clusters: 28,133

.file <- fig.dir %&% "/Fig_mtreg_DEG_count.pdf"
.gg.save(filename = .file, plot = plt, width=2, height=2)

PDF

hc.ms.deg[, c("ensembl_gene_id", "hgnc_symbol") := tstrsplit(`gene`, split="_")]

major.deg <- major.deg.tab[fwer < .05]$hgnc_symbol

.genes.show <-
    hc.ms.deg[hgnc_symbol %in% major.deg &
              sign(ADD) == sign(ADE) &
              sign(ADC) == sign(ADE)] %>%
    select(gene) %>%
    unique() %>%
    unlist() %>%
    as.character()

ensembl_gene_id	hgnc_symbol	z_1	z_2	z_3	pv_1	pv_2	pv_3	fdr_1	fdr_2	fdr_3	.link
	CD127	-6.22	1.99	-13.2	4.93e-10	4.65e-02	8.6e-40	7.23e-08	2.44e-01	6.71e-37	PDF
	CD137	-6.92	-13.97	-4.49	4.45e-12	2.27e-44	7.14e-06	8.18e-10	1.12e-41	6.02e-04	PDF
	CD161	3.77	-1.13	6.18	1.64e-04	2.6e-01	6.53e-10	6.4e-03	6.12e-01	1.22e-07	PDF
	CD183	17.84	9.76	6.37	3.31e-71	1.74e-22	1.94e-10	3.45e-68	4.41e-20	4.04e-08	PDF
	CD184	1.29	4.21	-0.53	1.96e-01	2.56e-05	5.96e-01	5.67e-01	9.11e-04	8.79e-01	PDF
	CD185	-4.67	-2.82	-6.22	2.99e-06	4.85e-03	4.89e-10	2.21e-04	5.75e-02	9.54e-08	PDF
	CD19	9.29	18.68	2.62	1.55e-20	6.85e-78	8.88e-03	6.07e-18	5.36e-75	1.21e-01	PDF
	CD194	1.84	-28.96	-21.08	6.64e-02	2.34e-184	1.23e-98	3.47e-01	4.39e-181	2.3e-95	PDF
	CD195	-5.69	-14.8	-1.44	1.26e-08	1.45e-49	1.51e-01	1.49e-06	8.01e-47	5.15e-01	PDF
	CD196	-24.65	-23.81	-16.68	3.92e-134	2.47e-125	1.7e-62	9.2e-131	2.58e-122	1.99e-59	PDF
	CD197	-1.19	-1.11	-4.41	2.34e-01	2.67e-01	1.02e-05	6.09e-01	6.18e-01	8.16e-04	PDF
	CD20	-5.72	-4.94	-6.08	1.05e-08	7.84e-07	1.17e-09	1.28e-06	4.33e-05	2.14e-07	PDF
	CD226	2.45	16.22	-7.39	1.43e-02	3.58e-59	1.43e-13	1.48e-01	2.4e-56	4.78e-11	PDF
	CD25	45.05	24.82	-10.21	0e+00	6.07e-136	1.83e-24	0e+00	7.13e-133	1.07e-21	PDF
	CD27	-71.81	-34.03	-72.37	0e+00	6.98e-254	0e+00	0e+00	2.18e-250	0e+00	PDF
	CD278	17.14	28.06	-7.04	7.37e-66	3.09e-173	1.96e-12	6.92e-63	4.14e-170	5.39e-10	PDF
	CD366	1.38	2.08	-1.18	1.68e-01	3.77e-02	2.36e-01	5.32e-01	2.17e-01	6.2e-01	PDF
	CD45RA	-20.35	-37.41	-43.66	4.95e-92	2.47e-306	0e+00	7.74e-89	1.16e-302	0e+00	PDF
	CD8a	-1.21	3.56	-3.73	2.28e-01	3.66e-04	1.93e-04	6.03e-01	8.12e-03	8.88e-03	PDF
ENSG00000003056	M6PR	-3.41	-4.75	-3.93	6.38e-04	2.02e-06	8.54e-05	1.83e-02	9.98e-05	4.76e-03	PDF
ENSG00000004468	CD38	NaN	-5.84	-0.89	Inf	5.1e-09	3.72e-01	Inf	3.92e-07	7.38e-01	PDF
ENSG00000008988	RPS20	-5.79	-7.38	-5.81	7.24e-09	1.53e-13	6.3e-09	9.18e-07	1.99e-11	1e-06	PDF
ENSG00000009790	TRAF3IP3	-6.77	-5.96	-6.31	1.29e-11	2.58e-09	2.82e-10	2.29e-09	2.05e-07	5.62e-08	PDF
ENSG00000009844	VTA1	-1.28	-2.92	-1.89	1.99e-01	3.5e-03	5.84e-02	5.73e-01	4.47e-02	3.3e-01	PDF
ENSG00000013573	DDX11	-1.47	-2.63	-2.09	1.43e-01	8.47e-03	3.62e-02	4.89e-01	8.16e-02	2.58e-01	PDF
ENSG00000019582	CD74	-2.52	-2.65	-1.8	1.18e-02	8.12e-03	7.14e-02	1.31e-01	7.94e-02	3.61e-01	PDF
ENSG00000025708	TYMP	1.38	1.68	0.73	1.68e-01	9.3e-02	4.66e-01	5.32e-01	3.64e-01	8.1e-01	PDF
ENSG00000026025	VIM	2.5	1.03	-1.4	1.24e-02	3.04e-01	1.62e-01	1.35e-01	6.53e-01	5.33e-01	PDF
ENSG00000026297	RNASET2	0.44	-2.24	-0.8	6.59e-01	2.49e-02	4.25e-01	9.05e-01	1.67e-01	7.8e-01	PDF
ENSG00000026508	CD44	1.68	0.86	-1.93	9.23e-02	3.89e-01	5.32e-02	4.04e-01	7.24e-01	3.14e-01	PDF
ENSG00000030582	GRN	0.24	0.02	-2.07	8.1e-01	9.84e-01	3.83e-02	9.55e-01	1e+00	2.65e-01	PDF
ENSG00000034510	TMSB10	2.87	-2.52	-5.35	4.06e-03	1.16e-02	8.88e-08	6.84e-02	1.01e-01	1.19e-05	PDF
ENSG00000036448	MYOM2	4.32	1.04	0.59	1.55e-05	3e-01	5.56e-01	9.08e-04	6.51e-01	8.58e-01	PDF
ENSG00000038274	MAT2B	-2.88	-5.11	-2.67	4.02e-03	3.26e-07	7.54e-03	6.83e-02	1.88e-05	1.09e-01	PDF
ENSG00000041357	PSMA4	-0.58	-2.9	-0.4	5.62e-01	3.76e-03	6.92e-01	8.57e-01	4.77e-02	9.21e-01	PDF
ENSG00000047410	TPR	-4.49	-4.5	-2.99	7.18e-06	6.75e-06	2.83e-03	4.83e-04	2.83e-04	5.96e-02	PDF
ENSG00000048405	ZNF800	-1.45	-2.89	-4.56	1.47e-01	3.86e-03	5.17e-06	4.99e-01	4.87e-02	4.61e-04	PDF
ENSG00000051108	HERPUD1	3.93	3.25	4.79	8.62e-05	1.14e-03	1.66e-06	3.76e-03	1.95e-02	1.67e-04	PDF
ENSG00000056558	TRAF1	-2.13	-3.71	-0.76	3.34e-02	2.06e-04	4.49e-01	2.41e-01	5.21e-03	7.98e-01	PDF
ENSG00000057657	PRDM1	2.93	3.51	1.06	3.4e-03	4.56e-04	2.91e-01	6.16e-02	9.74e-03	6.72e-01	PDF
ENSG00000059377	TBXAS1	0.57	4.26	0.33	5.69e-01	2.02e-05	7.39e-01	8.61e-01	7.45e-04	9.4e-01	PDF
ENSG00000059804	SLC2A3	-1.69	-1.96	-2.91	9.11e-02	5.02e-02	3.67e-03	4.02e-01	2.58e-01	7.14e-02	PDF
ENSG00000064666	CNN2	-1.63	-2.33	-0.89	1.02e-01	1.98e-02	3.72e-01	4.23e-01	1.44e-01	7.38e-01	PDF
ENSG00000064933	PMS1	-3.42	-2.53	-2.08	6.23e-04	1.15e-02	3.77e-02	1.8e-02	1e-01	2.63e-01	PDF
ENSG00000065978	YBX1	-3.31	-4.23	-2.8	9.22e-04	2.32e-05	5.1e-03	2.46e-02	8.31e-04	8.72e-02	PDF
ENSG00000066379	ZNRD1	-2.54	-3.52	-1.2	1.1e-02	4.25e-04	2.28e-01	1.27e-01	9.22e-03	6.13e-01	PDF
ENSG00000067082	KLF6	-3.97	-6.25	-1.68	7.15e-05	4.15e-10	9.23e-02	3.24e-03	3.78e-08	4.1e-01	PDF
ENSG00000069399	BCL3	2.77	3.6	1.06	5.54e-03	3.2e-04	2.89e-01	8.34e-02	7.34e-03	6.71e-01	PDF
ENSG00000069424	KCNAB2	-1.55	-1.37	-1.51	1.22e-01	1.7e-01	1.32e-01	4.57e-01	4.98e-01	4.82e-01	PDF
ENSG00000069493	CLEC2D	-2.38	-3.37	-3.8	1.71e-02	7.49e-04	1.47e-04	1.66e-01	1.43e-02	7.19e-03	PDF
ENSG00000071073	MGAT4A	2.44	1.87	3.37	1.47e-02	6.09e-02	7.39e-04	1.5e-01	2.88e-01	2.4e-02	PDF
ENSG00000073578	SDHA	-2.83	-4.75	-2.99	4.7e-03	1.99e-06	2.81e-03	7.46e-02	9.96e-05	5.93e-02	PDF
ENSG00000075624	ACTB	-14.21	-28.79	-12.14	7.56e-46	3.25e-182	6.84e-34	5.92e-43	5.08e-179	4.93e-31	PDF
ENSG00000077420	APBB1IP	-4	-4.35	-3.33	6.31e-05	1.38e-05	8.54e-04	2.98e-03	5.33e-04	2.66e-02	PDF
ENSG00000078304	PPP2R5C	-0.7	-1.75	-1.77	4.85e-01	7.98e-02	7.63e-02	8.13e-01	3.33e-01	3.73e-01	PDF
ENSG00000080824	HSP90AA1	-2.22	-8.39	-3.62	2.62e-02	5e-17	2.96e-04	2.11e-01	8.69e-15	1.21e-02	PDF
ENSG00000081059	TCF7	-3.88	-7.62	-5.2	1.03e-04	2.6e-14	1.95e-07	4.33e-03	3.59e-12	2.37e-05	PDF
ENSG00000081237	PTPRC	-4.56	-3.67	-3.28	5.19e-06	2.45e-04	1.03e-03	3.58e-04	6.05e-03	3.03e-02	PDF
ENSG00000083223	TUT7	-0.87	-2.64	-1	3.83e-01	8.35e-03	3.17e-01	7.45e-01	8.06e-02	6.94e-01	PDF
ENSG00000087074	PPP1R15A	3.2	1.27	-0.31	1.36e-03	2.03e-01	7.53e-01	3.23e-02	5.41e-01	9.48e-01	PDF
ENSG00000088986	DYNLL1	-4.42	-4.63	-4.43	9.69e-06	3.57e-06	9.25e-06	6.02e-04	1.64e-04	7.47e-04	PDF
ENSG00000090104	RGS1	0.83	4.39	-0.64	4.05e-01	1.11e-05	5.21e-01	7.62e-01	4.42e-04	8.4e-01	PDF
ENSG00000091317	CMTM6	-1.21	-1.4	1.95	2.26e-01	1.61e-01	5.17e-02	6.01e-01	4.84e-01	3.1e-01	PDF
ENSG00000092820	EZR	2.46	-0.98	-0.31	1.4e-02	3.25e-01	7.57e-01	1.45e-01	6.7e-01	9.5e-01	PDF
ENSG00000099985	OSM	-0.85	-0.31	-0.09	3.97e-01	7.57e-01	9.26e-01	7.56e-01	9.28e-01	1e+00	PDF
ENSG00000100097	LGALS1	2.46	-0.89	-1.89	1.39e-02	3.74e-01	5.81e-02	1.45e-01	7.13e-01	3.29e-01	PDF
ENSG00000100100	PIK3IP1	1.4	-0.41	-1.34	1.62e-01	6.84e-01	1.79e-01	5.22e-01	8.95e-01	5.53e-01	PDF
ENSG00000100129	EIF3L	-1.6	-6.5	-4.96	1.1e-01	7.96e-11	6.94e-07	4.36e-01	8.03e-09	7.64e-05	PDF
ENSG00000100201	DDX17	-4.72	-3.52	-3.96	2.35e-06	4.34e-04	7.62e-05	1.77e-04	9.34e-03	4.38e-03	PDF
ENSG00000100219	XBP1	2.77	2.31	0.98	5.67e-03	2.07e-02	3.25e-01	8.44e-02	1.49e-01	7e-01	PDF
ENSG00000100288	CHKB	1.01	3.32	0.58	3.13e-01	9.09e-04	5.64e-01	6.87e-01	1.66e-02	8.62e-01	PDF
ENSG00000100300	TSPO	2.23	4.51	1.95	2.54e-02	6.56e-06	5.14e-02	2.08e-01	2.78e-04	3.09e-01	PDF
ENSG00000100906	NFKBIA	7.15	6.08	4.4	8.43e-13	1.22e-09	1.06e-05	1.68e-10	1.02e-07	8.45e-04	PDF
ENSG00000101695	RNF125	0.57	0.18	-0.12	5.69e-01	8.53e-01	9.08e-01	8.61e-01	9.6e-01	1e+00	PDF
ENSG00000102007	PLP2	-1.77	1.23	-1.27	7.67e-02	2.2e-01	2.03e-01	3.7e-01	5.64e-01	5.84e-01	PDF
ENSG00000102109	PCSK1N	6.59	0.49	1	4.43e-11	6.24e-01	3.16e-01	7.42e-09	8.69e-01	6.93e-01	PDF
ENSG00000102226	USP11	-0.82	-0.47	-0.72	4.15e-01	6.35e-01	4.72e-01	7.68e-01	8.74e-01	8.13e-01	PDF
ENSG00000102245	CD40LG	-2.04	-0.09	-2.55	4.1e-02	9.32e-01	1.08e-02	2.69e-01	9.84e-01	1.35e-01	PDF
ENSG00000102760	RGCC	0.24	-5.21	0.15	8.07e-01	1.88e-07	8.84e-01	9.53e-01	1.11e-05	9.96e-01	PDF
ENSG00000102879	CORO1A	-8.89	-9.35	-6.99	5.91e-19	9.14e-21	2.73e-12	2.13e-16	2.09e-18	7.31e-10	PDF
ENSG00000103064	SLC7A6	-3.5	-2.68	-3.19	4.66e-04	7.32e-03	1.42e-03	1.46e-02	7.43e-02	3.77e-02	PDF
ENSG00000103121	CMC2	-2.51	-2.57	-2.26	1.21e-02	1.02e-02	2.39e-02	1.33e-01	9.31e-02	2.08e-01	PDF
ENSG00000103202	NME4	1.43	-0.28	-0.69	1.53e-01	7.79e-01	4.92e-01	5.08e-01	9.36e-01	8.24e-01	PDF
ENSG00000103479	RBL2	-2.91	-5.84	-3.52	3.59e-03	5.17e-09	4.27e-04	6.41e-02	3.94e-07	1.57e-02	PDF
ENSG00000103811	CTSH	1.29	3.94	0.14	1.98e-01	8.02e-05	8.86e-01	5.7e-01	2.41e-03	9.96e-01	PDF
ENSG00000104964	AES	-1.06	0.26	-3.63	2.9e-01	7.98e-01	2.89e-04	6.66e-01	9.42e-01	1.2e-02	PDF
ENSG00000105352	CEACAM4	0.61	1.01	0.29	5.45e-01	3.12e-01	7.72e-01	8.49e-01	6.59e-01	9.56e-01	PDF
ENSG00000105655	ISYNA1	-1.84	-1.98	-1.62	6.63e-02	4.8e-02	1.04e-01	3.46e-01	2.5e-01	4.34e-01	PDF
ENSG00000105835	NAMPT	-0.17	-0.67	0.29	8.64e-01	5.03e-01	7.75e-01	9.71e-01	8.02e-01	9.57e-01	PDF
ENSG00000106460	TMEM106B	-3.75	-2.04	-4.1	1.79e-04	4.17e-02	4.06e-05	6.9e-03	2.29e-01	2.57e-03	PDF
ENSG00000106560	GIMAP2	-4.49	-3.17	-3.55	7.25e-06	1.55e-03	3.93e-04	4.83e-04	2.47e-02	1.49e-02	PDF
ENSG00000106605	BLVRA	2.15	2.47	0.76	3.16e-02	1.34e-02	4.47e-01	2.33e-01	1.11e-01	7.98e-01	PDF
ENSG00000107738	VSIR	1.19	3.14	-1.64	2.36e-01	1.69e-03	1.01e-01	6.1e-01	2.64e-02	4.27e-01	PDF
ENSG00000107968	MAP3K8	0.48	1.36	-0.14	6.34e-01	1.75e-01	8.9e-01	8.95e-01	5.05e-01	9.97e-01	PDF
ENSG00000108518	PFN1	-7.25	-13.46	-6.86	4.11e-13	2.83e-41	6.96e-12	8.76e-11	1.21e-38	1.67e-09	PDF
ENSG00000108590	MED31	-3.48	-3.12	-3.04	4.93e-04	1.84e-03	2.38e-03	1.51e-02	2.78e-02	5.34e-02	PDF
ENSG00000108622	ICAM2	-7.61	-7.35	-5.59	2.78e-14	2.01e-13	2.32e-08	7.06e-12	2.58e-11	3.34e-06	PDF
ENSG00000109775	UFSP2	-2.47	-1.08	-0.74	1.36e-02	2.78e-01	4.62e-01	1.42e-01	6.29e-01	8.07e-01	PDF
ENSG00000109971	HSPA8	-7.92	-6.85	-7.56	2.34e-15	7.23e-12	4e-14	6.09e-13	8.27e-10	1.44e-11	PDF
ENSG00000110172	CHORDC1	-3.87	-1.65	-2.67	1.07e-04	9.82e-02	7.48e-03	4.43e-03	3.75e-01	1.09e-01	PDF
ENSG00000110848	CD69	-6.39	-0.07	-2.03	1.7e-10	9.41e-01	4.2e-02	2.61e-08	9.88e-01	2.76e-01	PDF
ENSG00000111348	ARHGDIB	-2.95	-8.76	-5.78	3.19e-03	2e-18	7.42e-09	5.96e-02	3.99e-16	1.16e-06	PDF
ENSG00000111640	GAPDH	-3.87	-15.55	-6.69	1.07e-04	1.59e-54	2.19e-11	4.43e-03	9.94e-52	5e-09	PDF
ENSG00000111679	PTPN6	-2.6	-3.05	-4.31	9.27e-03	2.29e-03	1.64e-05	1.14e-01	3.31e-02	1.22e-03	PDF
ENSG00000111796	KLRB1	2.94	1.56	5.33	3.33e-03	1.18e-01	9.72e-08	6.06e-02	4.12e-01	1.26e-05	PDF
ENSG00000112110	MRPL18	-3.4	-2.68	-2.44	6.78e-04	7.32e-03	1.47e-02	1.91e-02	7.43e-02	1.58e-01	PDF
ENSG00000112486	CCR6	-2.97	-0.31	-3.05	3.02e-03	7.55e-01	2.29e-03	5.74e-02	9.28e-01	5.18e-02	PDF
ENSG00000112773	TENT5A	0.97	0.97	0.79	3.34e-01	3.32e-01	4.32e-01	7.01e-01	6.76e-01	7.85e-01	PDF
ENSG00000113088	GZMK	2.43	-7.96	-2.38	1.51e-02	1.75e-15	1.71e-02	1.53e-01	2.74e-13	1.73e-01	PDF
ENSG00000113593	PPWD1	-0.95	-2.46	-1.89	3.43e-01	1.41e-02	5.88e-02	7.08e-01	1.15e-01	3.31e-01	PDF
ENSG00000113732	ATP6V0E1	-2.01	-1.98	-3.53	4.44e-02	4.82e-02	4.08e-04	2.83e-01	2.51e-01	1.53e-02	PDF
ENSG00000113749	HRH2	-2.56	-0.66	-0.91	1.06e-02	5.06e-01	3.62e-01	1.24e-01	8.05e-01	7.31e-01	PDF
ENSG00000115306	SPTBN1	-1.63	-6.61	-2.56	1.03e-01	3.9e-11	1.06e-02	4.24e-01	4.21e-09	1.33e-01	PDF
ENSG00000115687	PASK	3.24	1.63	1.32	1.18e-03	1.03e-01	1.88e-01	2.92e-02	3.84e-01	5.64e-01	PDF
ENSG00000115758	ODC1	3.29	0.51	3.15	9.94e-04	6.13e-01	1.61e-03	2.6e-02	8.66e-01	4.11e-02	PDF
ENSG00000116350	SRSF4	-2.65	-4.17	-2.86	7.96e-03	3.08e-05	4.25e-03	1.05e-01	1.07e-03	7.81e-02	PDF
ENSG00000116717	GADD45A	4.92	2.88	-0.2	8.47e-07	3.98e-03	8.42e-01	7.16e-05	4.99e-02	9.8e-01	PDF
ENSG00000116741	RGS2	1.82	-0.44	0.49	6.83e-02	6.61e-01	6.21e-01	3.51e-01	8.86e-01	8.89e-01	PDF
ENSG00000116754	SRSF11	-3.89	-3.77	-3.77	9.98e-05	1.62e-04	1.64e-04	4.26e-03	4.26e-03	7.81e-03	PDF
ENSG00000116815	CD58	-4.41	-0.87	-1.03	1.01e-05	3.85e-01	3.03e-01	6.25e-04	7.21e-01	6.83e-01	PDF
ENSG00000116824	CD2	-4.32	-6.19	-5.89	1.53e-05	6e-10	3.94e-09	9.01e-04	5.31e-08	6.35e-07	PDF
ENSG00000117091	CD48	-3.67	-5.41	-3.58	2.39e-04	6.25e-08	3.38e-04	8.44e-03	4.07e-06	1.33e-02	PDF
ENSG00000117318	ID3	-1.88	-1.45	-1.25	5.97e-02	1.46e-01	2.1e-01	3.27e-01	4.62e-01	5.92e-01	PDF
ENSG00000117448	AKR1A1	-2.17	-3.44	-1.69	3.02e-02	5.83e-04	9.14e-02	2.28e-01	1.19e-02	4.08e-01	PDF
ENSG00000117616	RSRP1	-2.59	-3.77	-2.47	9.48e-03	1.63e-04	1.36e-02	1.15e-01	4.27e-03	1.51e-01	PDF
ENSG00000118503	TNFAIP3	2.79	6.16	1.49	5.19e-03	7.28e-10	1.36e-01	8.01e-02	6.33e-08	4.91e-01	PDF
ENSG00000119138	KLF9	1.55	0.43	2.3	1.22e-01	6.7e-01	2.13e-02	4.57e-01	8.89e-01	1.97e-01	PDF
ENSG00000119185	ITGB1BP1	-3.77	-5.25	-3.7	1.65e-04	1.51e-07	2.2e-04	6.44e-03	9.25e-06	9.48e-03	PDF
ENSG00000119431	HDHD3	-3.96	-4.41	-3.93	7.45e-05	1.04e-05	8.41e-05	3.33e-03	4.18e-04	4.71e-03	PDF
ENSG00000119718	EIF2B2	-0.95	-1.74	-1.83	3.43e-01	8.23e-02	6.74e-02	7.09e-01	3.39e-01	3.52e-01	PDF
ENSG00000120833	SOCS2	-0.93	0.2	-1.06	3.51e-01	8.42e-01	2.91e-01	7.17e-01	9.56e-01	6.72e-01	PDF
ENSG00000120875	DUSP4	3.17	4.66	2.8	1.5e-03	3.24e-06	5.05e-03	3.46e-02	1.51e-04	8.63e-02	PDF
ENSG00000120913	PDLIM2	-3.39	-3.48	-3.27	7.01e-04	5.01e-04	1.09e-03	1.96e-02	1.05e-02	3.17e-02	PDF
ENSG00000121858	TNFSF10	-0.86	2.56	0.14	3.92e-01	1.05e-02	8.92e-01	7.51e-01	9.42e-02	9.98e-01	PDF
ENSG00000121966	CXCR4	3.97	4.49	-0.54	7.04e-05	6.99e-06	5.92e-01	3.21e-03	2.92e-04	8.76e-01	PDF
ENSG00000122224	LY9	-4.08	-1.89	-4.56	4.52e-05	5.91e-02	5.04e-06	2.21e-03	2.84e-01	4.54e-04	PDF
ENSG00000122862	SRGN	-1.09	-4.45	-0.86	2.75e-01	8.52e-06	3.91e-01	6.52e-01	3.52e-04	7.52e-01	PDF
ENSG00000123179	EBPL	-1.72	-1.87	-2.76	8.49e-02	6.21e-02	5.78e-03	3.91e-01	2.9e-01	9.4e-02	PDF
ENSG00000123219	CENPK	3.96	1.48	3.96	7.5e-05	1.39e-01	7.49e-05	3.34e-03	4.51e-01	4.34e-03	PDF
ENSG00000123416	TUBA1B	-6.5	-9.49	-3.06	8.01e-11	2.33e-21	2.18e-03	1.3e-08	5.47e-19	4.99e-02	PDF
ENSG00000124256	ZBP1	2.02	2.45	1.44	4.3e-02	1.43e-02	1.5e-01	2.78e-01	1.16e-01	5.13e-01	PDF
ENSG00000124575	HIST1H1D	0.94	1.73	1.22	3.46e-01	8.31e-02	2.23e-01	7.11e-01	3.4e-01	6.08e-01	PDF
ENSG00000124588	NQO2	-5.7	-5.19	-4.3	1.21e-08	2.1e-07	1.68e-05	1.45e-06	1.22e-05	1.23e-03	PDF
ENSG00000124766	SOX4	1.14	1.19	-0.54	2.52e-01	2.36e-01	5.92e-01	6.29e-01	5.83e-01	8.76e-01	PDF
ENSG00000124942	AHNAK	0.98	1.72	-1.64	3.28e-01	8.54e-02	1e-01	6.97e-01	3.47e-01	4.25e-01	PDF
ENSG00000125148	MT2A	-0.28	3.53	-2.42	7.81e-01	4.09e-04	1.56e-02	9.47e-01	8.93e-03	1.62e-01	PDF
ENSG00000125347	IRF1	-1.61	-3.08	-1.6	1.07e-01	2.04e-03	1.09e-01	4.31e-01	3.02e-02	4.45e-01	PDF
ENSG00000125384	PTGER2	1.18	-0.14	-1.04	2.38e-01	8.88e-01	2.97e-01	6.14e-01	9.72e-01	6.78e-01	PDF
ENSG00000125691	RPL23	-4.45	-3.02	-4.26	8.51e-06	2.49e-03	2.05e-05	5.47e-04	3.52e-02	1.43e-03	PDF
ENSG00000125726	CD70	2.71	3.46	0.48	6.75e-03	5.32e-04	6.33e-01	9.52e-02	1.1e-02	8.94e-01	PDF
ENSG00000125910	S1PR4	-4.5	-4.73	-3.91	6.91e-06	2.23e-06	9.17e-05	4.7e-04	1.08e-04	4.93e-03	PDF
ENSG00000125952	MAX	-2.63	-2.31	-2.83	8.66e-03	2.08e-02	4.62e-03	1.1e-01	1.49e-01	8.26e-02	PDF
ENSG00000126264	HCST	-3.71	-2.03	-3.58	2.04e-04	4.28e-02	3.48e-04	7.6e-03	2.32e-01	1.37e-02	PDF
ENSG00000126353	CCR7	-2.84	-9.84	-4.15	4.55e-03	7.72e-23	3.29e-05	7.39e-02	2.01e-20	2.14e-03	PDF
ENSG00000126524	SBDS	4	0.99	1.17	6.42e-05	3.24e-01	2.41e-01	3.01e-03	6.7e-01	6.25e-01	PDF
ENSG00000126709	IFI6	4.14	3.96	-0.42	3.44e-05	7.54e-05	6.76e-01	1.79e-03	2.28e-03	9.14e-01	PDF
ENSG00000127124	HIVEP3	-3.73	-1.46	-1.87	1.91e-04	1.43e-01	6.12e-02	7.26e-03	4.57e-01	3.37e-01	PDF
ENSG00000127528	KLF2	-0.88	-3.96	-3.77	3.81e-01	7.42e-05	1.6e-04	7.44e-01	2.25e-03	7.69e-03	PDF
ENSG00000128016	ZFP36	-1.29	0.73	-2.43	1.98e-01	4.63e-01	1.52e-02	5.71e-01	7.76e-01	1.6e-01	PDF
ENSG00000128536	CDHR3	1.13	1.76	1.67	2.6e-01	7.89e-02	9.46e-02	6.37e-01	3.32e-01	4.15e-01	PDF
ENSG00000128731	HERC2	-0.1	-1.31	-2.76	9.22e-01	1.91e-01	5.75e-03	9.84e-01	5.27e-01	9.39e-02	PDF
ENSG00000129824	RPS4Y1	-8.85	-3.44	-2.1	8.45e-19	5.79e-04	3.61e-02	2.83e-16	1.18e-02	2.58e-01	PDF
ENSG00000130066	SAT1	-3.23	-5.25	-3.19	1.24e-03	1.54e-07	1.41e-03	3.02e-02	9.42e-06	3.76e-02	PDF
ENSG00000130312	MRPL34	-4.17	-3.27	-2.53	3.01e-05	1.09e-03	1.14e-02	1.6e-03	1.89e-02	1.39e-01	PDF
ENSG00000130592	LSP1	0.17	2.11	-1.6	8.65e-01	3.48e-02	1.1e-01	9.72e-01	2.06e-01	4.46e-01	PDF
ENSG00000131981	LGALS3	-0.63	3.58	-0.06	5.29e-01	3.45e-04	9.55e-01	8.39e-01	7.77e-03	1e+00	PDF
ENSG00000132199	ENOSF1	-0.74	-1.31	-1.95	4.61e-01	1.89e-01	5.13e-02	7.97e-01	5.24e-01	3.09e-01	PDF
ENSG00000132406	TMEM128	-1.79	-3.5	-1.78	7.37e-02	4.63e-04	7.44e-02	3.64e-01	9.83e-03	3.7e-01	PDF
ENSG00000132965	ALOX5AP	-5.46	-0.91	-4.28	4.71e-08	3.64e-01	1.88e-05	5.33e-06	7.05e-01	1.32e-03	PDF
ENSG00000133321	RARRES3	-4.91	-6.73	-2.6	9.29e-07	1.72e-11	9.42e-03	7.67e-05	1.92e-09	1.25e-01	PDF
ENSG00000133561	GIMAP6	-2.83	-2.79	-3.49	4.68e-03	5.25e-03	4.88e-04	7.46e-02	6.05e-02	1.76e-02	PDF
ENSG00000133574	GIMAP4	-8.37	-11.37	-7.59	5.61e-17	6.2e-30	3.13e-14	1.6e-14	2.33e-27	1.2e-11	PDF
ENSG00000134184	GSTM1	-0.05	4.88	1.49	9.6e-01	1.08e-06	1.36e-01	9.93e-01	5.88e-05	4.9e-01	PDF
ENSG00000134882	UBAC2	-2.33	-3.02	-2.73	2e-02	2.56e-03	6.39e-03	1.81e-01	3.59e-02	9.91e-02	PDF
ENSG00000134905	CARS2	-0.26	-1.71	-0.55	7.97e-01	8.66e-02	5.8e-01	9.51e-01	3.5e-01	8.7e-01	PDF
ENSG00000135046	ANXA1	-5.33	-3.36	-6.18	9.77e-08	7.84e-04	6.37e-10	1.05e-05	1.48e-02	1.22e-07	PDF
ENSG00000135048	CEMIP2	1.21	2.65	0.19	2.28e-01	8.12e-03	8.48e-01	6.04e-01	7.94e-02	9.83e-01	PDF
ENSG00000135318	NT5E	4.16	0	0.02	3.19e-05	1e+00	9.88e-01	1.67e-03	1e+00	1e+00	PDF
ENSG00000135916	ITM2C	8.69	9.56	-0.32	3.67e-18	1.16e-21	7.46e-01	1.15e-15	2.78e-19	9.44e-01	PDF
ENSG00000136152	COG3	2.71	2.43	0.63	6.8e-03	1.51e-02	5.3e-01	9.55e-02	1.2e-01	8.43e-01	PDF
ENSG00000136213	CHST12	-0.1	-3.19	-1.12	9.21e-01	1.42e-03	2.63e-01	9.83e-01	2.31e-02	6.47e-01	PDF
ENSG00000136490	LIMD2	-7.03	-7.94	-6.04	1.99e-12	2.05e-15	1.57e-09	3.9e-10	3.16e-13	2.72e-07	PDF
ENSG00000136738	STAM	4.45	2.52	0.64	8.59e-06	1.18e-02	5.19e-01	5.49e-04	1.02e-01	8.39e-01	PDF
ENSG00000136810	TXN	-0.08	-0.35	-0.68	9.39e-01	7.26e-01	4.97e-01	9.9e-01	9.13e-01	8.27e-01	PDF
ENSG00000137038	DMAC1	-1.25	-4.57	-0.86	2.12e-01	4.91e-06	3.91e-01	5.88e-01	2.17e-04	7.53e-01	PDF
ENSG00000137078	SIT1	-5.34	-4.13	-5.97	9.37e-08	3.65e-05	2.3e-09	1.02e-05	1.23e-03	3.85e-07	PDF
ENSG00000137171	KLC4	-0.82	1.17	-1.35	4.14e-01	2.44e-01	1.76e-01	7.68e-01	5.93e-01	5.5e-01	PDF
ENSG00000137193	PIM1	0.93	-0.92	-0.14	3.54e-01	3.59e-01	8.85e-01	7.19e-01	7.01e-01	9.96e-01	PDF
ENSG00000137714	FDX1	0.57	-0.37	-1.19	5.7e-01	7.12e-01	2.35e-01	8.61e-01	9.09e-01	6.2e-01	PDF
ENSG00000138172	CALHM2	-3.08	-2.21	-2.5	2.04e-03	2.68e-02	1.26e-02	4.36e-02	1.74e-01	1.47e-01	PDF
ENSG00000138185	ENTPD1	4.97	4.28	5.63	6.56e-07	1.91e-05	1.82e-08	5.65e-05	7.05e-04	2.66e-06	PDF
ENSG00000138378	STAT4	-2.95	-3.14	-2.35	3.15e-03	1.7e-03	1.88e-02	5.89e-02	2.64e-02	1.83e-01	PDF
ENSG00000138640	FAM13A	-0.82	-2.08	-0.65	4.13e-01	3.77e-02	5.17e-01	7.67e-01	2.17e-01	8.37e-01	PDF
ENSG00000138757	G3BP2	4.17	0.58	2.08	3.02e-05	5.59e-01	3.75e-02	1.6e-03	8.37e-01	2.62e-01	PDF
ENSG00000138795	LEF1	-2.12	-2.04	-2.83	3.42e-02	4.17e-02	4.71e-03	2.44e-01	2.29e-01	8.34e-02	PDF
ENSG00000139187	KLRG1	2.19	1.01	-0.7	2.85e-02	3.12e-01	4.84e-01	2.2e-01	6.59e-01	8.2e-01	PDF
ENSG00000139192	TAPBPL	-3.39	-3.58	-1.05	7.08e-04	3.45e-04	2.93e-01	1.96e-02	7.77e-03	6.75e-01	PDF
ENSG00000139193	CD27	-1.23	-1.13	-3.95	2.18e-01	2.58e-01	7.83e-05	5.93e-01	6.08e-01	4.47e-03	PDF
ENSG00000139289	PHLDA1	2.77	2.08	1.3	5.53e-03	3.78e-02	1.92e-01	8.34e-02	2.17e-01	5.7e-01	PDF
ENSG00000139626	ITGB7	0.99	0.62	-2.03	3.24e-01	5.38e-01	4.26e-02	6.96e-01	8.24e-01	2.79e-01	PDF
ENSG00000139641	ESYT1	1.34	1.34	0.89	1.8e-01	1.81e-01	3.74e-01	5.46e-01	5.12e-01	7.4e-01	PDF
ENSG00000139679	LPAR6	-1.2	1.71	-0.89	2.32e-01	8.71e-02	3.76e-01	6.07e-01	3.51e-01	7.41e-01	PDF
ENSG00000140319	SRP14	2	-0.13	-0.95	4.52e-02	8.95e-01	3.42e-01	2.85e-01	9.74e-01	7.15e-01	PDF
ENSG00000140931	CMTM3	3.35	3.64	0.01	8.19e-04	2.68e-04	9.96e-01	2.22e-02	6.43e-03	1e+00	PDF
ENSG00000141556	TBCD	5.25	2.26	1.25	1.51e-07	2.38e-02	2.1e-01	1.49e-05	1.62e-01	5.92e-01	PDF
ENSG00000141682	PMAIP1	4.16	3.03	0.46	3.15e-05	2.48e-03	6.45e-01	1.66e-03	3.51e-02	9e-01	PDF
ENSG00000141959	PFKL	0.66	0.28	2.3	5.09e-01	7.8e-01	2.17e-02	8.27e-01	9.37e-01	1.98e-01	PDF
ENSG00000142188	TMEM50B	-1.57	-1.33	-2.67	1.17e-01	1.84e-01	7.65e-03	4.49e-01	5.15e-01	1.1e-01	PDF
ENSG00000142546	NOSIP	-5.01	-4.09	-3.87	5.39e-07	4.24e-05	1.07e-04	4.72e-05	1.38e-03	5.62e-03	PDF
ENSG00000143106	PSMA5	-3.61	-5.72	-1.81	3.08e-04	1.07e-08	6.96e-02	1.04e-02	7.76e-07	3.57e-01	PDF
ENSG00000143198	MGST3	5.28	5.95	2.93	1.28e-07	2.66e-09	3.4e-03	1.3e-05	2.1e-07	6.74e-02	PDF
ENSG00000143546	S100A8	-0.6	-0.09	-0.31	5.49e-01	9.27e-01	7.59e-01	8.52e-01	9.83e-01	9.51e-01	PDF
ENSG00000143641	GALNT2	3.02	2.31	2	2.55e-03	2.08e-02	4.52e-02	5.1e-02	1.49e-01	2.87e-01	PDF
ENSG00000144655	CSRNP1	2.8	1.07	0.19	5.16e-03	2.86e-01	8.51e-01	7.98e-02	6.37e-01	9.84e-01	PDF
ENSG00000144746	ARL6IP5	-2.56	-0.26	-3.63	1.04e-02	7.93e-01	2.83e-04	1.23e-01	9.4e-01	1.18e-02	PDF
ENSG00000145220	LYAR	-2.88	-2.71	-1.88	3.99e-03	6.64e-03	5.97e-02	6.8e-02	7.03e-02	3.32e-01	PDF
ENSG00000145391	SETD7	3.48	1.67	0.7	4.98e-04	9.48e-02	4.85e-01	1.52e-02	3.68e-01	8.2e-01	PDF
ENSG00000145649	GZMA	-5.61	-6.97	-4.61	2.04e-08	3.1e-12	4.1e-06	2.37e-06	3.69e-10	3.72e-04	PDF
ENSG00000145736	GTF2H2	-2.4	-0.72	-1.86	1.63e-02	4.7e-01	6.33e-02	1.61e-01	7.81e-01	3.41e-01	PDF
ENSG00000145779	TNFAIP8	-5.64	-3.12	-4.05	1.72e-08	1.82e-03	5.2e-05	2.02e-06	2.77e-02	3.22e-03	PDF
ENSG00000145860	RNF145	4.08	1.72	0.22	4.42e-05	8.6e-02	8.24e-01	2.17e-03	3.48e-01	9.74e-01	PDF
ENSG00000145945	FAM50B	-2.71	-2.97	-0.64	6.68e-03	2.98e-03	5.25e-01	9.46e-02	4.01e-02	8.41e-01	PDF
ENSG00000147138	GPR174	-0.23	-0.38	-1.8	8.15e-01	7.06e-01	7.19e-02	9.57e-01	9.07e-01	3.63e-01	PDF
ENSG00000147813	NAPRT	2.15	2.4	1.9	3.15e-02	1.63e-02	5.71e-02	2.32e-01	1.26e-01	3.25e-01	PDF
ENSG00000150347	ARID5B	3.32	3.53	1.88	9.04e-04	4.17e-04	5.96e-02	2.43e-02	9.05e-03	3.32e-01	PDF
ENSG00000150593	PDCD4	-2.94	-4.46	-3.47	3.3e-03	8.03e-06	5.21e-04	6.05e-02	3.33e-04	1.85e-02	PDF
ENSG00000150637	CD226	-0.02	1.14	-1.35	9.82e-01	2.53e-01	1.77e-01	9.99e-01	6.04e-01	5.5e-01	PDF
ENSG00000150753	CCT5	-4.33	-4.38	-1.81	1.48e-05	1.18e-05	6.95e-02	8.8e-04	4.63e-04	3.57e-01	PDF
ENSG00000152518	ZFP36L2	1.66	-2.53	-0.72	9.66e-02	1.15e-02	4.73e-01	4.11e-01	1e-01	8.13e-01	PDF
ENSG00000154165	GPR15	7.2	7.99	3.53	5.81e-13	1.31e-15	4.11e-04	1.19e-10	2.09e-13	1.53e-02	PDF
ENSG00000154229	PRKCA	-1.9	-1.9	-2.36	5.75e-02	5.78e-02	1.83e-02	3.21e-01	2.8e-01	1.8e-01	PDF
ENSG00000154451	GBP5	3.4	4.51	1.03	6.82e-04	6.45e-06	3.03e-01	1.91e-02	2.78e-04	6.83e-01	PDF
ENSG00000154767	XPC	-0.96	-0.77	-2.58	3.37e-01	4.39e-01	9.84e-03	7.03e-01	7.61e-01	1.28e-01	PDF
ENSG00000155959	VBP1	-3.76	-4.68	-3.31	1.67e-04	2.88e-06	9.25e-04	6.5e-03	1.35e-04	2.82e-02	PDF
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ENSG00000196230	TUBB	-4.8	-8.83	-3.91	1.56e-06	1.09e-18	9.06e-05	1.2e-04	2.27e-16	4.92e-03	PDF
ENSG00000196323	ZBTB44	-3.16	-3.72	-2.54	1.56e-03	2e-04	1.12e-02	3.51e-02	5.08e-03	1.38e-01	PDF
ENSG00000196329	GIMAP5	-1.75	-2.95	-3.29	8.01e-02	3.14e-03	9.88e-04	3.79e-01	4.13e-02	2.95e-02	PDF
ENSG00000196421	C20orf204	1.07	1.63	1.87	2.86e-01	1.03e-01	6.13e-02	6.62e-01	3.84e-01	3.37e-01	PDF
ENSG00000196787	HIST1H2AG	0.95	8.64	-1.49	3.44e-01	5.58e-18	1.36e-01	7.09e-01	1.07e-15	4.9e-01	PDF
ENSG00000196924	FLNA	-0.21	-1.42	-0.63	8.33e-01	1.55e-01	5.26e-01	9.63e-01	4.75e-01	8.42e-01	PDF
ENSG00000197061	HIST1H4C	-2.79	-7.83	-3.62	5.22e-03	4.89e-15	2.95e-04	8.02e-02	7.41e-13	1.21e-02	PDF
ENSG00000197329	PELI1	4.37	1.82	1.86	1.27e-05	6.93e-02	6.29e-02	7.74e-04	3.1e-01	3.4e-01	PDF
ENSG00000197448	GSTK1	-1.52	0.1	-1.77	1.29e-01	9.21e-01	7.61e-02	4.69e-01	9.82e-01	3.73e-01	PDF
ENSG00000197498	RPF2	-2.28	-0.85	-4.35	2.24e-02	3.93e-01	1.36e-05	1.93e-01	7.26e-01	1.03e-03	PDF
ENSG00000197540	GZMM	-4.01	-4.03	-2.78	6.14e-05	5.65e-05	5.44e-03	2.93e-03	1.76e-03	9.04e-02	PDF
ENSG00000197747	S100A10	-2.41	-0.07	-1.5	1.61e-02	9.46e-01	1.33e-01	1.6e-01	9.89e-01	4.84e-01	PDF
ENSG00000197928	ZNF677	-1.63	-0.59	-0.1	1.03e-01	5.56e-01	9.21e-01	4.25e-01	8.35e-01	1e+00	PDF
ENSG00000197956	S100A6	-2.4	5.57	-2.99	1.64e-02	2.56e-08	2.79e-03	1.62e-01	1.77e-06	5.93e-02	PDF
ENSG00000198189	HSD17B11	-1.63	-1.46	-1.66	1.04e-01	1.44e-01	9.74e-02	4.26e-01	4.58e-01	4.21e-01	PDF
ENSG00000198417	MT1F	-1.19	-3.37	-2.45	2.35e-01	7.59e-04	1.42e-02	6.09e-01	1.44e-02	1.55e-01	PDF
ENSG00000198502	HLA-DRB5	-6.6	-5.22	-4.88	4.04e-11	1.78e-07	1.05e-06	6.89e-09	1.06e-05	1.1e-04	PDF
ENSG00000198763	MT-ND2	6.1	-0.99	-0.59	1.07e-09	3.2e-01	5.56e-01	1.47e-07	6.66e-01	8.58e-01	PDF
ENSG00000198771	RCSD1	-2.07	-4.75	-2.05	3.82e-02	2.01e-06	4.03e-02	2.58e-01	9.98e-05	2.69e-01	PDF
ENSG00000198805	PNP	-3.48	-3.63	-4.29	4.94e-04	2.83e-04	1.8e-05	1.51e-02	6.7e-03	1.29e-03	PDF
ENSG00000198830	HMGN2	3.47	-4.34	-0.49	5.29e-04	1.43e-05	6.26e-01	1.59e-02	5.47e-04	8.91e-01	PDF
ENSG00000204161	TMEM273	-5.31	-2.11	-2.03	1.11e-07	3.44e-02	4.21e-02	1.15e-05	2.05e-01	2.76e-01	PDF
ENSG00000204261	PSMB8-AS1	-3.55	-2.86	-1.98	3.83e-04	4.27e-03	4.73e-02	1.25e-02	5.24e-02	2.95e-01	PDF
ENSG00000204287	HLA-DRA	-0.1	-3.57	-1.6	9.21e-01	3.61e-04	1.09e-01	9.83e-01	8.04e-03	4.43e-01	PDF
ENSG00000204389	HSPA1A	-4.81	-3.79	-4.28	1.52e-06	1.48e-04	1.83e-05	1.18e-04	3.99e-03	1.3e-03	PDF
ENSG00000204472	AIF1	-0.44	-5.79	-3.68	6.61e-01	7e-09	2.34e-04	9.06e-01	5.22e-07	1e-02	PDF
ENSG00000204677	FAM153C	-1.32	-0.17	-1.35	1.88e-01	8.67e-01	1.76e-01	5.56e-01	9.64e-01	5.5e-01	PDF
ENSG00000205138	SDHAF1	-4.1	-2.86	-2.7	4.09e-05	4.27e-03	6.87e-03	2.03e-03	5.24e-02	1.04e-01	PDF
ENSG00000205268	PDE7A	-2.3	-4.35	-1.69	2.13e-02	1.39e-05	9.1e-02	1.88e-01	5.33e-04	4.07e-01	PDF
ENSG00000205707	ETFRF1	-3.08	-3.6	-2.74	2.05e-03	3.17e-04	6.2e-03	4.36e-02	7.3e-03	9.81e-02	PDF
ENSG00000211706	TRBV6-1	-11.75	-3.75	-7.51	7.39e-32	1.76e-04	5.73e-14	4.33e-29	4.55e-03	1.99e-11	PDF
ENSG00000211710	TRBV4-1	10.47	9.94	4.51	1.21e-25	2.85e-23	6.47e-06	5.39e-23	7.79e-21	5.61e-04	PDF
ENSG00000211716	TRBV9	8.48	-1.11	1.13	2.27e-17	2.67e-01	2.6e-01	6.7e-15	6.18e-01	6.44e-01	PDF
ENSG00000211721	TRBV6-5	-1.64	-7.33	-1.22	1.01e-01	2.28e-13	2.22e-01	4.21e-01	2.89e-11	6.07e-01	PDF
ENSG00000211724	TRBV6-6	-4.45	11.06	-1.16	8.68e-06	1.94e-28	2.46e-01	5.51e-04	6.99e-26	6.3e-01	PDF
ENSG00000211727	TRBV7-6	1.64	-0.97	0.8	1.01e-01	3.32e-01	4.25e-01	4.21e-01	6.76e-01	7.8e-01	PDF
ENSG00000211734	TRBV5-1	-2.13	6.43	-1.66	3.29e-02	1.24e-10	9.78e-02	2.39e-01	1.22e-08	4.21e-01	PDF
ENSG00000211745	TRBV4-2	7.01	0.11	-0.03	2.36e-12	9.14e-01	9.8e-01	4.52e-10	9.8e-01	1e+00	PDF
ENSG00000211747	TRBV20-1	1.56	4.24	-0.13	1.19e-01	2.25e-05	8.96e-01	4.52e-01	8.1e-04	9.98e-01	PDF
ENSG00000211751	TRBC1	-6.11	-8.72	-5.4	1e-09	2.83e-18	6.62e-08	1.4e-07	5.54e-16	9.11e-06	PDF
ENSG00000211753	TRBV28	4.88	6.33	0.72	1.05e-06	2.47e-10	4.69e-01	8.59e-05	2.36e-08	8.11e-01	PDF
ENSG00000211779	TRAV5	-4.44	1.46	-1.9	8.89e-06	1.45e-01	5.77e-02	5.6e-04	4.61e-01	3.27e-01	PDF
ENSG00000211780	TRAV6	-1.62	-3.27	-2.05	1.06e-01	1.06e-03	4.07e-02	4.29e-01	1.87e-02	2.7e-01	PDF
ENSG00000211782	TRAV8-1	-6.46	-3.01	-0.66	1.06e-10	2.66e-03	5.12e-01	1.66e-08	3.7e-02	8.36e-01	PDF
ENSG00000211786	TRAV8-2	-3.73	-1.47	-2.73	1.9e-04	1.41e-01	6.38e-03	7.23e-03	4.54e-01	9.91e-02	PDF
ENSG00000211788	TRAV13-1	-5.32	-0.52	-5.93	1.05e-07	6.06e-01	3.11e-09	1.1e-05	8.64e-01	5.1e-07	PDF
ENSG00000211789	TRAV12-2	6.21	6.96	4.17	5.34e-10	3.3e-12	3.09e-05	7.71e-08	3.87e-10	2.04e-03	PDF
ENSG00000211794	TRAV12-3	3.37	4.39	-2.79	7.48e-04	1.13e-05	5.23e-03	2.06e-02	4.47e-04	8.82e-02	PDF
ENSG00000211795	TRAV8-6	-3.96	-2.97	-0.69	7.36e-05	3.03e-03	4.87e-01	3.3e-03	4.05e-02	8.22e-01	PDF
ENSG00000211796	TRAV16	-1.44	0.27	-3.72	1.5e-01	7.87e-01	2.01e-04	5.02e-01	9.39e-01	8.98e-03	PDF
ENSG00000211801	TRAV21	-2.73	1.53	-3.62	6.27e-03	1.25e-01	3e-04	9.01e-02	4.26e-01	1.21e-02	PDF
ENSG00000211810	TRAV29DV5	-6.54	-7.77	-3.28	6.21e-11	7.69e-15	1.03e-03	1.02e-08	1.11e-12	3.03e-02	PDF
ENSG00000211812	TRAV26-2	-1.3	-9.94	-7.32	1.94e-01	2.78e-23	2.52e-13	5.64e-01	7.79e-21	7.62e-11	PDF
ENSG00000211817	TRAV38-2DV8	-3.99	-10.8	-0.3	6.75e-05	3.46e-27	7.61e-01	3.09e-03	1.16e-24	9.51e-01	PDF
ENSG00000211820	TRAV41	0.48	1.25	0.65	6.29e-01	2.13e-01	5.17e-01	8.91e-01	5.55e-01	8.38e-01	PDF
ENSG00000213145	CRIP1	-1.2	2.66	-1.81	2.31e-01	7.91e-03	7e-02	6.07e-01	7.83e-02	3.57e-01	PDF
ENSG00000213203	GIMAP1	-1.92	-4.41	-3.31	5.43e-02	1.03e-05	9.22e-04	3.13e-01	4.15e-04	2.82e-02	PDF
ENSG00000213402	PTPRCAP	1.59	3.21	0.19	1.13e-01	1.31e-03	8.49e-01	4.41e-01	2.19e-02	9.83e-01	PDF
ENSG00000213626	LBH	-5.85	-4.13	-3.34	4.87e-09	3.61e-05	8.28e-04	6.43e-07	1.22e-03	2.62e-02	PDF
ENSG00000215845	TSTD1	-3.67	-4.12	-4.06	2.47e-04	3.85e-05	4.96e-05	8.65e-03	1.27e-03	3.11e-03	PDF
ENSG00000226067	LINC00623	-0.34	-1.71	-1.51	7.3e-01	8.76e-02	1.31e-01	9.33e-01	3.52e-01	4.81e-01	PDF
ENSG00000226660	TRBV2	10.27	4.71	-4.24	9.4e-25	2.47e-06	2.2e-05	4.01e-22	1.19e-04	1.53e-03	PDF
ENSG00000227507	LTB	0.61	-6	-6.08	5.4e-01	2.02e-09	1.23e-09	8.45e-01	1.65e-07	2.16e-07	PDF
ENSG00000230099	TRBV5-4	-8.32	-5.39	-6.94	8.43e-17	7.23e-08	4.05e-12	2.33e-14	4.62e-06	1.03e-09	PDF
ENSG00000231682	LINC01891	-3.4	-4.38	-3.2	6.78e-04	1.2e-05	1.36e-03	1.91e-02	4.68e-04	3.65e-02	PDF
ENSG00000232869	TRBV29-1	-1.01	-2	3.09	3.12e-01	4.51e-02	2.02e-03	6.86e-01	2.4e-01	4.76e-02	PDF
ENSG00000235532	LINC00402	-3.97	-4.4	-3	7.19e-05	1.08e-05	2.69e-03	3.24e-03	4.32e-04	5.83e-02	PDF
ENSG00000237541	HLA-DQA2	-4.6	-2.08	0.21	4.16e-06	3.72e-02	8.31e-01	2.96e-04	2.15e-01	9.76e-01	PDF
ENSG00000237702	TRBV3-1	7.3	-0.7	-4.37	2.98e-13	4.86e-01	1.26e-05	6.67e-11	7.92e-01	9.7e-04	PDF
ENSG00000240065	PSMB9	-3.48	-5.44	-2.6	4.95e-04	5.33e-08	9.31e-03	1.51e-02	3.6e-06	1.24e-01	PDF
ENSG00000240972	MIF	-0.18	-7.79	-2.42	8.58e-01	6.76e-15	1.56e-02	9.7e-01	9.92e-13	1.62e-01	PDF
ENSG00000241343	RPL36A	-1.45	-5.67	-1.95	1.48e-01	1.4e-08	5.14e-02	5e-01	1e-06	3.09e-01	PDF
ENSG00000241657	TRBV11-2	-0.67	4.82	1.04	5.05e-01	1.43e-06	2.97e-01	8.24e-01	7.47e-05	6.78e-01	PDF
ENSG00000242086	MUC20-OT1	-2.77	-4.37	-2.5	5.62e-03	1.26e-05	1.25e-02	8.43e-02	4.9e-04	1.47e-01	PDF
ENSG00000243749	TMEM35B	-2.9	-4.52	-2.08	3.74e-03	6.25e-06	3.73e-02	6.49e-02	2.7e-04	2.61e-01	PDF
ENSG00000243927	MRPS6	-4.34	-4.92	-3.32	1.39e-05	8.58e-07	9.05e-04	8.39e-04	4.71e-05	2.79e-02	PDF
ENSG00000244734	HBB	0.44	2.56	0.11	6.62e-01	1.05e-02	9.14e-01	9.06e-01	9.42e-02	1e+00	PDF
ENSG00000245532	NEAT1	-5.3	-4.68	-4.55	1.15e-07	2.84e-06	5.41e-06	1.17e-05	1.34e-04	4.77e-04	PDF
ENSG00000245904	AC025164.1	-2.5	-3.09	-2.01	1.23e-02	2.01e-03	4.48e-02	1.34e-01	3e-02	2.86e-01	PDF
ENSG00000246223	LINC01550	-2.54	-4.44	-3.07	1.09e-02	9.1e-06	2.13e-03	1.27e-01	3.75e-04	4.92e-02	PDF
ENSG00000250303	AP002884.1	1.76	-0.59	-0.16	7.86e-02	5.57e-01	8.75e-01	3.75e-01	8.35e-01	9.93e-01	PDF
ENSG00000253738	OTUD6B-AS1	-1.32	-3.42	-1.26	1.87e-01	6.22e-04	2.09e-01	5.56e-01	1.24e-02	5.91e-01	PDF
ENSG00000254999	BRK1	-2.67	-0.12	-3.76	7.52e-03	9.05e-01	1.67e-04	1.01e-01	9.78e-01	7.91e-03	PDF
ENSG00000260708	AL118516.1	2.48	-1.43	2.05	1.3e-02	1.54e-01	4.07e-02	1.39e-01	4.74e-01	2.7e-01	PDF
ENSG00000266338	NBPF15	-2.62	-1.94	-2.47	8.92e-03	5.22e-02	1.35e-02	1.12e-01	2.64e-01	1.51e-01	PDF
ENSG00000268027	AC243960.1	-2.48	-4.08	-1.59	1.3e-02	4.52e-05	1.12e-01	1.39e-01	1.44e-03	4.47e-01	PDF
ENSG00000269028	MTRNR2L12	-4.64	-7.79	-9.56	3.48e-06	6.48e-15	1.2e-21	2.53e-04	9.66e-13	6.25e-19	PDF
ENSG00000271109	AC008555.5	-3.18	-1.79	-1.45	1.48e-03	7.33e-02	1.47e-01	3.43e-02	3.2e-01	5.1e-01	PDF
ENSG00000271503	CCL5	1.16	-1.83	-2.48	2.46e-01	6.75e-02	1.31e-02	6.24e-01	3.06e-01	1.49e-01	PDF
ENSG00000275074	NUDT18	-3.82	-3.06	-2.11	1.36e-04	2.19e-03	3.5e-02	5.41e-03	3.2e-02	2.53e-01	PDF
ENSG00000275791	TRBV10-3	-7.59	-8.53	0.08	3.11e-14	1.46e-17	9.38e-01	7.68e-12	2.69e-15	1e+00	PDF
ENSG00000276557	TRBV18	5.24	1.33	1.75	1.6e-07	1.82e-01	7.97e-02	1.56e-05	5.13e-01	3.83e-01	PDF
ENSG00000276953	TRBV12-4	7.36	12.67	-7.09	1.81e-13	8.48e-37	1.31e-12	4.15e-11	3.46e-34	3.73e-10	PDF
ENSG00000277734	TRAC	-3.27	-1.81	-0.81	1.06e-03	6.97e-02	4.17e-01	2.71e-02	3.1e-01	7.75e-01	PDF
ENSG00000278030	TRBV7-9	7.23	-2.33	2.05	4.81e-13	2e-02	4.02e-02	1e-10	1.45e-01	2.69e-01	PDF
ENSG00000280721	LINC01943	2.71	3.38	1.86	6.81e-03	7.22e-04	6.26e-02	9.56e-02	1.4e-02	3.4e-01	PDF
ENSG00000283063	TRBV6-2	-11.04	-0.08	-6.32	2.4e-28	9.35e-01	2.67e-10	1.19e-25	9.85e-01	5.44e-08	PDF
ENSG00000283782	AC116366.3	-5.3	-2.82	-2.58	1.14e-07	4.84e-03	9.74e-03	1.17e-05	5.75e-02	1.28e-01	PDF
ENSG00000285437	POLR2J3	0	-1.28	-1.84	1e+00	2.01e-01	6.54e-02	1e+00	5.38e-01	3.46e-01	PDF
	TCRab	-22.96	-8.4	-15.92	1.29e-116	4.55e-17	4.78e-57	2.42e-113	8.07e-15	4.97e-54	PDF
	TIGIT	-18.59	-4.42	-9.69	3.58e-77	9.86e-06	3.26e-22	4.2e-74	3.99e-04	1.79e-19	PDF

Additional genes/proteins

ensembl_gene_id	hgnc_symbol	z_1	z_2	z_3	pv_1	pv_2	pv_3	fdr_1	fdr_2	fdr_3	.link
	CD27	-71.81	-34.03	-72.37	0e+00	6.98e-254	0e+00	0e+00	2.18e-250	0e+00	PDF
	CD279	2.96	5.42	-2.91	3.06e-03	6.07e-08	3.62e-03	5.78e-02	3.99e-06	7.08e-02	PDF
	CD366	1.38	2.08	-1.18	1.68e-01	3.77e-02	2.36e-01	5.32e-01	2.17e-01	6.2e-01	PDF
ENSG00000009790	TRAF3IP3	-6.77	-5.96	-6.31	1.29e-11	2.58e-09	2.82e-10	2.29e-09	2.05e-07	5.62e-08	PDF
ENSG00000049768	FOXP3	0.21	-1.31	-1.21	8.33e-01	1.92e-01	2.26e-01	9.63e-01	5.27e-01	6.11e-01	PDF
ENSG00000089692	LAG3	0	6.59	-1	1e+00	4.48e-11	3.15e-01	1e+00	4.73e-09	6.93e-01	PDF
ENSG00000118515	SGK1	1.13	0.97	1.24	2.6e-01	3.34e-01	2.14e-01	6.38e-01	6.78e-01	5.97e-01	PDF
ENSG00000124191	TOX2	0.53	-2.47	-0.35	5.96e-01	1.36e-02	7.27e-01	8.74e-01	1.12e-01	9.35e-01	PDF
ENSG00000135077	HAVCR2	0	0.44	0.72	1e+00	6.59e-01	4.71e-01	1e+00	8.86e-01	8.12e-01	PDF
ENSG00000139193	CD27	-1.23	-1.13	-3.95	2.18e-01	2.58e-01	7.83e-05	5.93e-01	6.08e-01	4.47e-03	PDF
ENSG00000178562	CD28	-0.72	-5.46	-1.29	4.73e-01	4.88e-08	1.96e-01	8.05e-01	3.32e-06	5.75e-01	PDF
ENSG00000188389	PDCD1	0.37	-0.85	-1.35	7.08e-01	3.93e-01	1.78e-01	9.25e-01	7.26e-01	5.51e-01	PDF
ENSG00000198846	TOX	1.57	2.66	-2.21	1.16e-01	7.9e-03	2.68e-02	4.46e-01	7.83e-02	2.21e-01	PDF

Step 5: differential Expression analysis for sub clusters

Yongjin Park

2024-03-06

1. mTconv subtype DEG analysis

Gene-level statistics confirm that some genes are not expressed much

Creating Q/C’ed DEG data

Found 817 unique genes strongly perturbed by MS with FDR 10%

Examples

Additional genes/proteins

2. mTreg subtype DEG analysis

Gene-level statistics confirm that some genes are not expressed much

Creating Q/C’ed DEG data

Found 1,703 unique genes strongly perturbed by MS with FDR 10%

Additional genes/proteins