Coexpression cluster:C3965

Full id: C3965_cerebellum_CD4_pineal_small_merkel_Neutrophils_CD8

Phase1 CAGE Peaks

Hg19::chr1:29241027..29241095,+	p2@EPB41
Hg19::chr1:29241108..29241121,+	p5@EPB41
Hg19::chr1:29241128..29241159,+	p3@EPB41

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
hematopoietic stem cell	8.45e-18	168
angioblastic mesenchymal cell	8.45e-18	168
hematopoietic cell	3.27e-16	177
hematopoietic oligopotent progenitor cell	1.62e-15	161
hematopoietic multipotent progenitor cell	1.62e-15	161
lymphocyte	1.94e-15	53
common lymphoid progenitor	1.94e-15	53
lymphoid lineage restricted progenitor cell	4.63e-15	52
nucleate cell	1.22e-14	55
mature alpha-beta T cell	2.31e-12	18
alpha-beta T cell	2.31e-12	18
immature T cell	2.31e-12	18
mature T cell	2.31e-12	18
immature alpha-beta T cell	2.31e-12	18
leukocyte	2.47e-11	136
T cell	3.35e-10	25
pro-T cell	3.35e-10	25
nongranular leukocyte	6.52e-10	115
CD8-positive, alpha-beta T cell	3.35e-08	11
hematopoietic lineage restricted progenitor cell	1.91e-07	120

Uber Anatomy

Ontology term	p-value	n
adult organism	3.64e-08	114
blood	8.42e-08	15
haemolymphatic fluid	8.42e-08	15
organism substance	8.42e-08	15

Disease

Ontology term	p-value	n
hematologic cancer	9.75e-08	51
immune system cancer	9.75e-08	51
leukemia	1.53e-07	39
germ cell and embryonal cancer	1.82e-07	22
germ cell cancer	1.82e-07	22

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	0.0190215736718214
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325652054055771
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437578501406423
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032257322746792
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462737038077546
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00898191938792985
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108806516001304
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128196787791861
MAX#4149	3	6.45255550900712	0.00372191383426551	0.018673758596121
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00720825464746168
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294797531864168
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199841564057236
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246052667338729
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00471475417877798
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00485016213344648
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277101977670245
SP1#6667	3	5.6983813781409	0.00540396270171217	0.024677938810849
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000940941535195575
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00543620879181857
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190461692832044
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421918696384765
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140344590543135

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.