Coexpression cluster:C4535

Full id: C4535_Neutrophils_CD4_CD8_Peripheral_Eosinophils_CD34_Natural

Phase1 CAGE Peaks

Hg19::chr5:98264458..98264477,-	p@chr5:98264458..98264477 -
Hg19::chr5:98264490..98264505,-	p@chr5:98264490..98264505 -
Hg19::chr5:98264529..98264538,-	p@chr5:98264529..98264538 -

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><br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	3.02e-30	168
angioblastic mesenchymal cell	3.02e-30	168
hematopoietic cell	1.38e-28	177
leukocyte	3.20e-28	136
hematopoietic oligopotent progenitor cell	1.50e-26	161
hematopoietic multipotent progenitor cell	1.50e-26	161
hematopoietic lineage restricted progenitor cell	4.27e-22	120
nongranular leukocyte	2.99e-21	115
myeloid cell	8.50e-15	108
common myeloid progenitor	8.50e-15	108
classical monocyte	1.96e-14	42
CD14-positive, CD16-negative classical monocyte	1.96e-14	42
myeloid leukocyte	6.67e-14	72
nucleate cell	3.41e-12	55
lymphocyte	1.43e-11	53
common lymphoid progenitor	1.43e-11	53
granulocyte monocyte progenitor cell	3.20e-11	67
lymphoid lineage restricted progenitor cell	3.46e-11	52
defensive cell	5.48e-11	48
phagocyte	5.48e-11	48
myeloid lineage restricted progenitor cell	1.55e-10	66
macrophage dendritic cell progenitor	1.34e-09	61
monopoietic cell	7.87e-09	59
monocyte	7.87e-09	59
monoblast	7.87e-09	59
promonocyte	7.87e-09	59

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	3.37e-12	98
blood island	3.37e-12	98
hemolymphoid system	4.61e-09	108
bone element	5.01e-09	82
bone marrow	1.20e-08	76
skeletal element	2.70e-07	90
immune system	6.26e-07	93

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	0.019093233011732
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327292436268134
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438624803544714
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323976049449151
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.032214539782541
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464564656286116
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00764641989275624
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00389254770070175
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.00085401929494252
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109092554390609
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128625845404903
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.0047306968527021
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173573559699834
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.006451246624754
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00545190321482866
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000722127867594195
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330949793326744
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140780653448342

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.