Coexpression cluster:C272

Full id: C272_CD19_CD4_CD8_Whole_Peripheral_lymph_tonsil

Phase1 CAGE Peaks

Hg19::chr10:111836795..111836820,+	p5@ADD3
Hg19::chr11:10562868..10562896,+	p1@ENST00000529979
Hg19::chr11:64511738..64511759,+	p@chr11:64511738..64511759 +
Hg19::chr11:64512273..64512337,-	p3@RASGRP2
Hg19::chr11:94964744..94964758,+	p1@ENST00000540692
Hg19::chr12:103835454..103835475,-	p4@C12orf42
Hg19::chr12:103835494..103835510,-	p5@C12orf42
Hg19::chr12:12867280..12867310,+	p@chr12:12867280..12867310 +
Hg19::chr12:92539858..92539862,+	p1@uc001tca.2
Hg19::chr12:92539926..92539990,+	p1@ENST00000499685
Hg19::chr12:92540055..92540069,+	p@chr12:92540055..92540069 +
Hg19::chr13:103498907..103498922,-	p@chr13:103498907..103498922 -
Hg19::chr15:75081804..75081827,-	p@chr15:75081804..75081827 -
Hg19::chr15:89178835..89178856,+	p7@ISG20
Hg19::chr15:89178857..89178898,+	p3@ISG20
Hg19::chr17:26874766..26874781,-	p5@UNC119
Hg19::chr17:38020516..38020544,-	p5@IKZF3
Hg19::chr17:76128488..76128519,-	p4@TMC6
Hg19::chr19:16482478..16482486,-	p@chr19:16482478..16482486 -
Hg19::chr19:50004358..50004377,-	p2@MIR150
Hg19::chr19:7413915..7413935,+	p@chr19:7413915..7413935 +
Hg19::chr1:157670686..157670730,-	p2@FCRL3
Hg19::chr1:157670738..157670753,-	p3@FCRL3
Hg19::chr1:207085241..207085281,-	p@chr1:207085241..207085281 -
Hg19::chr1:207095279..207095310,-	p1@FAIM3
Hg19::chr1:207095324..207095357,-	p2@FAIM3
Hg19::chr1:207096529..207096554,-	p5@FAIM3
Hg19::chr1:207096713..207096727,+	p@chr1:207096713..207096727 +
Hg19::chr20:57698436..57698458,+	p@chr20:57698436..57698458 +
Hg19::chr20:62266805..62266812,-	p@chr20:62266805..62266812 -
Hg19::chr20:62273068..62273079,-	p10@STMN3
Hg19::chr20:62273138..62273178,-	p5@STMN3
Hg19::chr2:234327537..234327560,+	p6@DGKD
Hg19::chr3:32433154..32433217,+	p3@CMTM7
Hg19::chr3:71355163..71355209,-	p5@FOXP1
Hg19::chr5:118668891..118668933,+	p5@TNFAIP8
Hg19::chr6:133084580..133084605,-	p2@VNN2
Hg19::chr6:24936227..24936236,-	p5@FAM65B
Hg19::chr6:26285304..26285323,-	p12@HIST1H4H
Hg19::chr6:31540403..31540430,-	p1@LOC100287329
Hg19::chr7:139929994..139930043,+	p@chr7:139929994..139930043 +
Hg19::chr7:99819057..99819097,+	p@chr7:99819057..99819097 +
Hg19::chr8:134511587..134511621,-	p6@ST3GAL1
Hg19::chr9:36144997..36145021,-	p@chr9:36144997..36145021 -
Hg19::chrX:134429952..134429971,-	p3@ZNF75D
Hg19::chrX:78200673..78200687,-	p@chrX:78200673..78200687 -
Hg19::chrX:78200857..78200909,+	p1@P2RY10

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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p.value	FDR	nGenes	nPathway	Name
0.000142706552983131	0.0451666240191609	3	133	T Cell Receptor Signaling Pathway (Wikipathways):WP69
7.05821870032124e-05	0.0446785243730334	4	295	IL-2 down reg. targets (Netpath):NetPath_14

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
lymphocyte	1.33e-55	53
common lymphoid progenitor	1.33e-55	53
lymphoid lineage restricted progenitor cell	2.87e-54	52
nucleate cell	5.17e-53	55
leukocyte	1.94e-39	136
nongranular leukocyte	2.02e-37	115
hematopoietic lineage restricted progenitor cell	2.00e-30	120
mature alpha-beta T cell	2.36e-29	18
alpha-beta T cell	2.36e-29	18
immature T cell	2.36e-29	18
mature T cell	2.36e-29	18
immature alpha-beta T cell	2.36e-29	18
hematopoietic stem cell	4.84e-28	168
angioblastic mesenchymal cell	4.84e-28	168
lymphocyte of B lineage	6.02e-27	24
pro-B cell	6.02e-27	24
hematopoietic cell	1.34e-25	177
hematopoietic oligopotent progenitor cell	2.76e-24	161
hematopoietic multipotent progenitor cell	2.76e-24	161
T cell	1.15e-23	25
pro-T cell	1.15e-23	25
B cell	1.25e-20	14
CD8-positive, alpha-beta T cell	1.92e-18	11
CD4-positive, alpha-beta T cell	2.13e-11	6
intermediate monocyte	3.79e-07	9
CD14-positive, CD16-positive monocyte	3.79e-07	9
naive T cell	9.73e-07	3

Uber Anatomy

Ontology term	p-value	n
blood	8.76e-15	15
haemolymphatic fluid	8.76e-15	15
organism substance	8.76e-15	15
hemopoietic organ	3.87e-08	7
immune organ	3.87e-08	7
hematopoietic system	1.05e-07	98
blood island	1.05e-07	98
hemolymphoid system	1.31e-07	108
thymus	4.83e-07	4
hemolymphoid system gland	4.83e-07	4
thymic region	4.83e-07	4
pharyngeal gland	4.83e-07	4
thymus primordium	4.83e-07	4

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BCL11A#53335	11	6.63965970509952	5.56664771744241e-07	2.57473481382626e-05
BCLAF1#9774	7	3.22486241001815	0.0055380719997451	0.0250700317099986
CHD2#1106	10	2.20085592215252	0.013032274459842	0.0462385416602609
EBF1#1879	19	3.60048659754917	2.70249283007159e-07	1.39105790379422e-05
ELF1#1997	20	1.81195657821597	0.00296219731129923	0.0157897680291318
GATA1#2623	9	2.59665475094051	0.00672772114817381	0.0285950052496388
MEF2A#4205	11	4.38671361715074	2.88179123592645e-05	0.000603754051933645
MEF2C#4208	8	7.03171991363814	1.58699131059788e-05	0.000371123568041944
NFKB1#4790	23	2.68564805864805	1.61968458039418e-06	6.14673829548646e-05
PAX5#5079	14	1.9866790943934	0.00738149095180661	0.0305047298795398
PBX3#5090	8	3.73012981902028	0.00119505309143275	0.00810718738656347
POLR2A#5430	41	1.87331021784853	6.97304015138524e-09	5.43070350761016e-07
POU2F2#5452	16	3.09995712604001	2.33354936079437e-05	0.000509115441178197
RAD21#5885	10	2.20319870116092	0.0129413240333475	0.0465179466776382
RDBP#7936	3	9.80670663766116	0.00360346113913373	0.0182424565152684
SPI1#6688	25	4.36400186623549	1.34287519443163e-11	1.6558269472402e-09
SREBF2#6721	3	27.8899954730647	0.000179078841470122	0.0021719678462778
TAF1#6872	25	1.77821610943899	0.000717973017093988	0.00573669833465527
TBP#6908	22	1.73508415140682	0.00281411859658068	0.0154037595444596
TCF12#6938	12	2.71518252821781	0.00107755915767746	0.00760862692641989
ZEB1#6935	9	3.23395506718925	0.00155742540525139	0.00988850093616934

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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