Coexpression cluster:C3547

Full id: C3547_granulocyte_acute_Eosinophils_salivary_hepatoblastoma_cerebellum_tridermal

Phase1 CAGE Peaks

Hg19::chr16:2802623..2802721,+	p1@SRRM2
Hg19::chr19:5622779..5622813,-	p1@SAFB2
Hg19::chr19:5623083..5623158,+	p1@SAFB

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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GO ID	GO name	FDR corrected p-value
GO:0003723	RNA binding	0.00137547276961258

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	8.18e-33	168
angioblastic mesenchymal cell	8.18e-33	168
hematopoietic cell	5.89e-31	177
hematopoietic oligopotent progenitor cell	7.21e-31	161
hematopoietic multipotent progenitor cell	7.21e-31	161
leukocyte	1.15e-24	136
myeloid cell	3.62e-23	108
common myeloid progenitor	3.62e-23	108
hematopoietic lineage restricted progenitor cell	6.94e-19	120
nongranular leukocyte	1.99e-17	115
classical monocyte	2.51e-15	42
CD14-positive, CD16-negative classical monocyte	2.51e-15	42
myeloid leukocyte	1.47e-14	72
granulocyte monocyte progenitor cell	3.90e-12	67
myeloid lineage restricted progenitor cell	1.74e-11	66
defensive cell	4.43e-11	48
phagocyte	4.43e-11	48
macrophage dendritic cell progenitor	3.68e-10	61
monopoietic cell	1.40e-09	59
monocyte	1.40e-09	59
monoblast	1.40e-09	59
promonocyte	1.40e-09	59
nucleate cell	6.26e-08	55
lymphocyte	1.70e-07	53
common lymphoid progenitor	1.70e-07	53
lymphoid lineage restricted progenitor cell	1.96e-07	52

Uber Anatomy

Ontology term	p-value	n
adult organism	2.97e-22	114
neural tube	1.73e-14	56
neural rod	1.73e-14	56
future spinal cord	1.73e-14	56
neural keel	1.73e-14	56
regional part of nervous system	8.53e-14	53
regional part of brain	8.53e-14	53
hematopoietic system	4.43e-13	98
blood island	4.43e-13	98
nervous system	6.58e-12	89
regional part of forebrain	1.47e-11	41
forebrain	1.47e-11	41
anterior neural tube	1.47e-11	41
future forebrain	1.47e-11	41
central nervous system	2.00e-11	81
brain	4.20e-11	68
future brain	4.20e-11	68
hemolymphoid system	6.01e-11	108
neurectoderm	1.31e-10	86
neural plate	4.73e-10	82
presumptive neural plate	4.73e-10	82
bone element	1.31e-09	82
brain grey matter	1.32e-09	34
gray matter	1.32e-09	34
telencephalon	1.38e-09	34
bone marrow	1.47e-09	76
regional part of telencephalon	5.11e-09	32
cerebral hemisphere	1.15e-08	32
immune system	1.21e-08	93
pre-chordal neural plate	5.69e-08	61
regional part of cerebral cortex	1.62e-07	22
neocortex	6.27e-07	20

Disease

Ontology term	p-value	n
leukemia	1.46e-07	39
myeloid leukemia	3.43e-07	31
hematologic cancer	4.07e-07	51
immune system cancer	4.07e-07	51

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	0.0189732219339672
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324718645015373
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436537179118528
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321532183145662
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461348195671311
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186281189886833
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294017362767451
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000736877543471443
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269248407178878
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470585768635761
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00881137231975336
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276151171654304
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00541892287895487
THAP1#55145	2	20.9127630685675	0.00298344741373694	0.0158641751664005
YY1#7528	3	4.91117074985386	0.00844145534180826	0.032874082871322
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00388567113123133

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.