Coexpression cluster:C3091

Full id: C3091_granulocyte_Neutrophils_optic_skeletal_Eosinophils_immature_CD4

Phase1 CAGE Peaks

Hg19::chr11:11863500..11863576,+	p1@USP47
Hg19::chr1:179923875..179923954,+	p1@CEP350
Hg19::chr8:42752053..42752154,+	p1@HOOK3

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:0031122	cytoplasmic microtubule organization and biogenesis	0.00304662663369834
GO:0051645	Golgi localization	0.00304662663369834
GO:0015630	microtubule cytoskeleton	0.0157887649980403
GO:0005801	cis-Golgi network	0.018273841294435
GO:0044430	cytoskeletal part	0.0296554642569538
GO:0051640	organelle localization	0.0334813341011192
GO:0008017	microtubule binding	0.0425925335828027
GO:0005856	cytoskeleton	0.043737425088151
GO:0015631	tubulin binding	0.0452728129930291
GO:0005819	spindle	0.0474197284120837

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
leukocyte	1.58e-35	140
hematopoietic stem cell	5.20e-33	172
angioblastic mesenchymal cell	5.20e-33	172
hematopoietic oligopotent progenitor cell	1.44e-30	165
hematopoietic multipotent progenitor cell	1.44e-30	165
hematopoietic cell	4.21e-28	182
hematopoietic lineage restricted progenitor cell	1.51e-27	124
nongranular leukocyte	3.39e-25	119
myeloid leukocyte	3.58e-24	76
myeloid cell	3.61e-23	112
common myeloid progenitor	3.61e-23	112
granulocyte monocyte progenitor cell	6.16e-22	71
myeloid lineage restricted progenitor cell	4.01e-20	70
macrophage dendritic cell progenitor	8.03e-19	65
CD14-positive, CD16-negative classical monocyte	4.93e-18	42
monopoietic cell	1.27e-17	63
monocyte	1.27e-17	63
monoblast	1.27e-17	63
promonocyte	1.27e-17	63
classical monocyte	7.99e-17	45
lymphoid lineage restricted progenitor cell	2.82e-07	52
lymphocyte	3.42e-07	53
common lymphoid progenitor	3.42e-07	53
mature alpha-beta T cell	6.27e-07	18
alpha-beta T cell	6.27e-07	18
immature T cell	6.27e-07	18
mature T cell	6.27e-07	18
immature alpha-beta T cell	6.27e-07	18

Uber Anatomy

Ontology term	p-value	n
adult organism	1.78e-28	115
hematopoietic system	7.22e-21	102
blood island	7.22e-21	102
hemolymphoid system	5.80e-18	112
bone marrow	3.94e-17	80
bone element	4.96e-17	86
skeletal element	7.67e-14	101
skeletal system	7.67e-14	101
neural tube	2.30e-13	57
neural rod	2.30e-13	57
future spinal cord	2.30e-13	57
neural keel	2.30e-13	57
immune system	1.14e-12	115
anterior neural tube	1.38e-11	42
regional part of brain	1.58e-11	59
regional part of forebrain	2.93e-11	41
forebrain	2.93e-11	41
future forebrain	2.93e-11	41
brain	3.28e-11	69
future brain	3.28e-11	69
central nervous system	1.09e-10	82
regional part of nervous system	6.21e-09	94
nervous system	6.21e-09	94
gray matter	1.13e-08	34
brain grey matter	1.13e-08	34
telencephalon	2.84e-08	34
regional part of telencephalon	3.70e-08	33
cerebral hemisphere	1.35e-07	32

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
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296095885820155
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323600852777799
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460092826431389
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.015573220527912
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108300324334896
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268607366797856
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172290661632547
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00879456207049469
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275425094954074
XRCC4#7518	1	1432.76744186046	0.000697791383889146	0.00561150645584034
ZBTB33#10009	2	21.1098166866541	0.00292859706060324	0.0156282125804681

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.