Coexpression cluster:C2855

Full id: C2855_Tracheal_blood_Hodgkin_carcinoid_CD4_Reticulocytes_chronic

Phase1 CAGE Peaks

Hg19::chr6:26056231..26056264,+	p2@CU678091
Hg19::chr6:26157017..26157056,-	p@chr6:26157017..26157056 -
Hg19::chr6:26157065..26157123,-	p@chr6:26157065..26157123 -
Hg19::chr6:26157179..26157224,-	p@chr6:26157179..26157224 -

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><br>disease_data<br>

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Cell Type

Ontology term	p-value	n
nucleate cell	1.21e-07	55
lymphocyte	6.58e-07	53
common lymphoid progenitor	6.58e-07	53

Disease

Ontology term	p-value	n
cancer	5.26e-18	235
disease of cellular proliferation	1.92e-16	239
hematologic cancer	1.96e-11	51
immune system cancer	1.96e-11	51
organ system cancer	5.01e-10	137
cell type cancer	2.53e-09	143
leukemia	1.94e-07	39

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
BCL3#602	2	17.2735514018692	0.00483449420807607	0.0226813593548024
BCLAF1#9774	4	21.6526476101218	4.54636978835329e-06	0.000141821479786687
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00819559495357511
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101626912126555
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.00154779890299911
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378807892994997
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186552001214016
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00392465335355418
POU2F2#5452	4	9.10612405774252	0.00014539566517493	0.00188727042943133
REST#5978	3	7.23752153709602	0.00410469730419261	0.0195945919075131
RXRA#6256	4	20.0746171391333	6.1537798808435e-06	0.000182583698004379
SRF#6722	3	10.3478836966259	0.00143989377840126	0.00924170761568641
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0323244272927976
TAF7#6879	4	11.4330694049239	5.85061525419808e-05	0.00097189821303196
TCF7L2#6934	3	8.07763242235301	0.00297838168583462	0.0158719871867987
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0483384285011919
USF2#7392	4	12.9921973850696	3.50833029870167e-05	0.000682702642195088
ZBTB33#10009	4	31.6647250299812	9.93721537730495e-07	4.20856787019607e-05
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342571776549043
ZEB1#6935	4	16.8884320175439	1.22862303393937e-05	0.000305078842229182

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.