Coexpression cluster:C4700

Full id: C4700_thymus_adrenal_Whole_acute_CD4_Burkitt_Reticulocytes

Phase1 CAGE Peaks

Hg19::chr7:75932863..75932900,+	p4@HSPB1
Hg19::chr7:75932909..75932923,+	p6@HSPB1
Hg19::chr7:75932929..75932953,+	p5@HSPB1

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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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>disease_data<br>

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Cell Type

Ontology term	p-value	n
lymphocyte	9.07e-20	53
common lymphoid progenitor	9.07e-20	53
lymphoid lineage restricted progenitor cell	3.16e-19	52
T cell	4.19e-11	25
pro-T cell	4.19e-11	25
mature alpha-beta T cell	2.25e-09	18
alpha-beta T cell	2.25e-09	18
immature T cell	2.25e-09	18
mature T cell	2.25e-09	18
immature alpha-beta T cell	2.25e-09	18
lymphocyte of B lineage	2.28e-08	24
pro-B cell	2.28e-08	24
CD8-positive, alpha-beta T cell	8.58e-08	11
hematopoietic cell	7.45e-07	182

Uber Anatomy

Ontology term	p-value	n
blood	2.40e-09	15
haemolymphatic fluid	2.40e-09	15
organism substance	2.40e-09	15

Disease

Ontology term	p-value	n
hematologic cancer	1.10e-10	51
immune system cancer	1.10e-10	51
leukemia	3.42e-09	39
myeloid leukemia	3.13e-08	31
organ system cancer	1.50e-07	137

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0191136792525025
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662828937382171
CTBP2#1488	3	62.7170003393281	4.049570681927e-06	0.000130575212241363
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327729425019595
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324293685483358
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322466395040888
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464947894582299
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00256409978659123
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168506260683288
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00765261174367148
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154817060229127
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.0038947198813383
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109204892261263
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128731791683585
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157686324110273
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187430907438572
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00723491348938778
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296071186709903
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000741327603236634
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270841251530517
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00310278236050586
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00473460167882896
REST#5978	3	9.65002871612802	0.00111263624711459	0.0077134163300631
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278270395521781
SP1#6667	3	5.6983813781409	0.00540396270171217	0.024788495283034
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00645588947946775
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000722794037213747
YY1#7528	3	4.91117074985386	0.00844145534180826	0.033124822635473
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140908978976954
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.011013502259213

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.