Coexpression cluster:C2306

Full id: C2306_CD4_CD8_cerebellum_Mast_Neural_thymus_Natural

Phase1 CAGE Peaks

Hg19::chr14:64108537..64108597,-	p1@WDR89
Hg19::chr2:120517452..120517509,+	p1@PTPN4
Hg19::chr2:120517517..120517541,+	p2@PTPN4
Hg19::chr2:242041691..242041740,-	p1@MTERFD2

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:0004726	non-membrane spanning protein tyrosine phosphatase activity	0.00927234192864712

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
nucleate cell	1.15e-21	55
lymphocyte	5.63e-21	53
common lymphoid progenitor	5.63e-21	53
lymphoid lineage restricted progenitor cell	1.62e-20	52
mature alpha-beta T cell	1.89e-12	18
alpha-beta T cell	1.89e-12	18
immature T cell	1.89e-12	18
mature T cell	1.89e-12	18
immature alpha-beta T cell	1.89e-12	18
T cell	6.77e-12	25
pro-T cell	6.77e-12	25
CD8-positive, alpha-beta T cell	1.68e-08	11
lymphocyte of B lineage	2.57e-08	24
pro-B cell	2.57e-08	24
B cell	1.58e-07	14

Uber Anatomy

Ontology term	p-value	n
adult organism	4.46e-22	114
central nervous system	1.48e-13	81
nervous system	1.72e-12	89
neural tube	1.55e-11	56
neural rod	1.55e-11	56
future spinal cord	1.55e-11	56
neural keel	1.55e-11	56
regional part of nervous system	2.47e-11	53
regional part of brain	2.47e-11	53
regional part of forebrain	3.12e-11	41
forebrain	3.12e-11	41
anterior neural tube	3.12e-11	41
future forebrain	3.12e-11	41
brain	3.47e-10	68
future brain	3.47e-10	68
telencephalon	5.90e-09	34
organ system subdivision	1.37e-08	223
brain grey matter	1.39e-08	34
gray matter	1.39e-08	34
regional part of telencephalon	2.35e-08	32
cerebral hemisphere	2.44e-08	32
blood	3.44e-07	15
haemolymphatic fluid	3.44e-07	15
organism substance	3.44e-07	15
cerebral cortex	7.95e-07	25
pallium	7.95e-07	25

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
BCLAF1#9774	2	10.8263238050609	0.0120220381643258	0.0436507316035329
BRCA1#672	3	15.1381729824178	0.000468218442143119	0.00430043671435979
CHD2#1106	4	10.3440228341169	8.73193255208051e-05	0.00128971051309113
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00995873060857629
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160699088665264
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418802148729277
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0192015519194203
GATA1#2623	3	10.1702311078503	0.00151515816849827	0.00966124940227066
GTF2B#2959	2	15.9719149671621	0.00563658572353722	0.0254696221338858
GTF2F1#2962	3	9.55474565756824	0.00182036231930478	0.0108974447017008
HDAC2#3066	3	10.0617151774697	0.0015637275447474	0.00992308549312636
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185738714756561
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.00247824451456598
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319984324045566
IRF4#3662	2	10.9572563433721	0.0117453018068803	0.0428275810142021
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0386751865563592
MAFF#23764	2	28.1576782449726	0.00184687618036715	0.0109240471994883
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466063868330421
MEF2A#4205	3	14.057423182233	0.000583003885418661	0.00488670487875116
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00886520988399882
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.0076726401722997
NFYA#4800	3	13.8191855248729	0.000613241180673451	0.00508586481921342
NR3C1#2908	3	11.2297674983798	0.00113167206806385	0.00775376888516177
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00443413731187851
RFX5#5993	4	12.0479108271951	4.74457429336527e-05	0.000825864324374626
RXRA#6256	3	15.05596285435	0.000475830799730358	0.00433754847630609
SETDB1#9869	3	30.2400196335079	5.98509618524166e-05	0.000984528997464882
SMARCB1#6598	3	13.6895368358681	0.000630578340937934	0.0051806931520781
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00683379723197223
SPI1#6688	3	6.15324263139204	0.00658038711305903	0.0280957053963768
SREBF2#6721	1	109.235815602837	0.00912320148412682	0.034516139822522
SRF#6722	4	13.7971782621678	2.75840773062708e-05	0.000583641298579743
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321652549186544
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140285450262667
TAL1#6886	2	14.9343083387201	0.00642807757788807	0.0279434753031031
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243774361023429
TCF7L2#6934	4	10.7701765631373	7.42969445082454e-05	0.00115228669252994
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00507321201078031
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106687208883638
ZBTB33#10009	3	23.7485437724859	0.000122945190881838	0.00165488758738346
ZEB1#6935	4	16.8884320175439	1.22862303393937e-05	0.000303778790344683
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00248260623933188

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.