Coexpression cluster:C4177

Full id: C4177_lung_bile_mesenchymal_somatostatinoma_testicular_hepatoma_large

Phase1 CAGE Peaks

Hg19::chr2:209118929..209118940,-	p8@IDH1
Hg19::chr2:209118956..209118973,-	p2@IDH1
Hg19::chr2:209118974..209118991,-	p7@IDH1

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
fat cell	1.61e-08	15

Uber Anatomy

Ontology term	p-value	n
body cavity	8.69e-07	46

Disease

Ontology term	p-value	n
disease of cellular proliferation	3.17e-28	239
cancer	1.42e-26	235
cell type cancer	1.27e-20	143
carcinoma	8.15e-18	106
organ system cancer	1.44e-09	137
myeloid leukemia	1.77e-07	31

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	0.0190471675861945
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115462911948973
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280171545264744
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00172060238405987
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.032138251578633
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463482237350791
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167799312031935
ESRRA#2101	3	483.840314136126	8.75956906834516e-09	6.72182684738354e-07
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00243450175007005
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00388640632613916
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434835027061683
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108905837330379
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123003258954014
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000757913965072842
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295189171097321
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000738834201844973
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309475606049859
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173265971801769
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00883557938656587
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00665720968394633
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165438330803632
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277463136438704
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00309774369648633
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247081893268592
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00375729200150785
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00630221479286284
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00615179400620762
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00248737507219323
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00617073733580925
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190766230903728
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330119506643868
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.014053221700108
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389780716085303

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.