Coexpression cluster:C4782

Full id: C4782_small_gastrointestinal_medulloblastoma_Hodgkin_hepatoblastoma_anaplastic_acute

Phase1 CAGE Peaks

Hg19::chr8:95907993..95908004,+	p6@C8orf38
Hg19::chr8:95908020..95908035,+	p3@C8orf38
Hg19::chr8:95908044..95908055,+	p4@C8orf38

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
nucleate cell	4.89e-11	55
lymphocyte	1.99e-10	53
common lymphoid progenitor	1.99e-10	53
lymphoid lineage restricted progenitor cell	4.05e-10	52

Uber Anatomy

Ontology term	p-value	n
neural tube	3.65e-08	56
neural rod	3.65e-08	56
future spinal cord	3.65e-08	56
neural keel	3.65e-08	56
regional part of nervous system	9.92e-08	53
regional part of brain	9.92e-08	53
brain	1.09e-07	68
future brain	1.09e-07	68
nervous system	2.17e-07	89
brain grey matter	4.65e-07	34
gray matter	4.65e-07	34
organ system subdivision	5.93e-07	223

Disease

Ontology term	p-value	n
cancer	1.32e-37	235
disease of cellular proliferation	8.62e-36	239
cell type cancer	3.76e-24	143
carcinoma	4.76e-21	106
organ system cancer	5.88e-19	137
hematologic cancer	7.67e-16	51
immune system cancer	7.67e-16	51
leukemia	5.29e-14	39
myeloid leukemia	2.01e-11	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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0281567633024555
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0328070112745623
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324662924465651
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465283747147868
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00765881363067925
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00902376150531776
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.0058461912417106
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107754480243645
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154922471729833
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00393930570085341
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128823753069006
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187530373859926
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00723838370964444
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296346401408781
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00200345305846361
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246846827311219
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00137436766255222
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00486954379586198
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278528771005088
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0248091986726501
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0141067822101036

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.