Coexpression cluster:C871

Full id: C871_CD19_Mast_CD4_CD8_Natural_Peripheral_Basophils

Phase1 CAGE Peaks

Hg19::chr10:27531947..27531980,-	p@chr10:27531947..27531980 -
Hg19::chr15:52471650..52471680,+	p@chr15:52471650..52471680 +
Hg19::chr1:231473624..231473639,-	p2@EXOC8
Hg19::chr1:31191601..31191660,+	p1@LOC100129196
Hg19::chr2:202123066..202123088,-	p@chr2:202123066..202123088 -
Hg19::chr4:40198642..40198689,+	p1@RHOH
Hg19::chr5:43484423..43484517,-	p2@C5orf28
Hg19::chr8:41998304..41998320,-	p@chr8:41998304..41998320 -
Hg19::chr9:6757183..6757204,+	p9@KDM4C

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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No results for this coexpression

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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GO ID	GO name	FDR corrected p-value
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.0384038116999737
GO:0005095	GTPase inhibitor activity	0.0384038116999737

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
leukocyte	1.45e-40	136
hematopoietic stem cell	2.64e-40	168
angioblastic mesenchymal cell	2.64e-40	168
hematopoietic cell	6.23e-37	177
hematopoietic oligopotent progenitor cell	1.07e-35	161
hematopoietic multipotent progenitor cell	1.07e-35	161
hematopoietic lineage restricted progenitor cell	7.45e-33	120
nucleate cell	8.92e-33	55
lymphocyte	9.33e-32	53
common lymphoid progenitor	9.33e-32	53
lymphoid lineage restricted progenitor cell	1.16e-31	52
nongranular leukocyte	3.17e-30	115
T cell	2.66e-15	25
pro-T cell	2.66e-15	25
lymphocyte of B lineage	4.10e-15	24
pro-B cell	4.10e-15	24
mature alpha-beta T cell	3.29e-14	18
alpha-beta T cell	3.29e-14	18
immature T cell	3.29e-14	18
mature T cell	3.29e-14	18
immature alpha-beta T cell	3.29e-14	18
B cell	1.36e-11	14
myeloid cell	3.01e-10	108
common myeloid progenitor	3.01e-10	108
CD8-positive, alpha-beta T cell	2.31e-09	11
myeloid leukocyte	2.02e-08	72
granulocyte monocyte progenitor cell	5.55e-07	67
intermediate monocyte	8.06e-07	9
CD14-positive, CD16-positive monocyte	8.06e-07	9

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	5.17e-13	98
blood island	5.17e-13	98
adult organism	2.28e-12	114
hemolymphoid system	8.52e-12	108
blood	3.65e-09	15
haemolymphatic fluid	3.65e-09	15
organism substance	3.65e-09	15
immune system	9.93e-07	93

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
BRF2#55290	1	119.397286821705	0.00834447063348787	0.0328553503672324
E2F6#1876	7	3.90223223576463	0.000306742359949273	0.00316153807665471
ELF1#1997	7	3.31185396796142	0.000896020581017362	0.00666853085305154
GTF2F1#2962	4	5.66207150078118	0.0034642002070655	0.0176014403028807
HEY1#23462	6	2.69340736207047	0.00948764347376227	0.0357421634295083
IRF4#3662	3	7.30483756224804	0.00648299961540963	0.0281459094127771
MAX#4149	7	5.01865428478332	5.77474544696214e-05	0.000962049194026605
MEF2A#4205	3	6.24774363654802	0.0100000500846256	0.0374966872792234
MXI1#4601	4	4.42736516833747	0.00844465741513493	0.0327765562575917
MYC#4609	8	4.64202833031947	1.34916872863392e-05	0.000327155404805661
NFKB1#4790	6	3.65870894946256	0.00185064964860272	0.0109327449884281
POLR2A#5430	9	2.14745317655807	0.00102941289260802	0.00728343967827989
POU2F2#5452	6	6.07074937182835	0.000109527229587528	0.00152356344311292
SIN3A#25942	7	4.20691034307844	0.000186784365617447	0.00225991338747922
SMC3#9126	4	6.68663681997015	0.00187316159335173	0.0110420005445652
TAF1#6872	9	3.34304628574529	1.91655056102793e-05	0.000433346230879403
TBP#6908	7	2.88304386774163	0.00218780200212605	0.0126147989455111
TCF12#6938	4	4.72642884541619	0.00668035530260397	0.0284179718727814
YY1#7528	7	3.81979947210855	0.000352967281214194	0.00353539367821322

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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This analysis result is provided for C0 - C305 clusters.