Coexpression cluster:C4459

Full id: C4459_Eosinophils_Neutrophils_CD14_occipital_postcentral_parietal_medial

Phase1 CAGE Peaks

Hg19::chr5:130599701..130599716,+	p2@CDC42SE2
Hg19::chr7:97736163..97736190,+	p1@LMTK2
Hg19::chr7:97736234..97736245,+	p2@LMTK2

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:0004864	protein phosphatase inhibitor activity	0.0243568701007585
GO:0019212	phosphatase inhibitor activity	0.0243568701007585
GO:0016301	kinase activity	0.0243568701007585
GO:0046777	protein amino acid autophosphorylation	0.0243568701007585
GO:0016540	protein autoprocessing	0.0243568701007585
GO:0016772	transferase activity, transferring phosphorus-containing groups	0.0249784497864923
GO:0019888	protein phosphatase regulator activity	0.0271223419769981
GO:0019208	phosphatase regulator activity	0.0271223419769981
GO:0016485	protein processing	0.0290996119542236
GO:0016740	transferase activity	0.0416052735611413

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	2.89e-14	140
hematopoietic stem cell	1.59e-11	172
angioblastic mesenchymal cell	1.59e-11	172
hematopoietic oligopotent progenitor cell	8.84e-11	165
hematopoietic multipotent progenitor cell	8.84e-11	165
hematopoietic lineage restricted progenitor cell	2.45e-10	124
hematopoietic cell	5.56e-10	182
nongranular leukocyte	7.43e-10	119
classical monocyte	2.04e-07	45
CD14-positive, CD16-negative classical monocyte	2.79e-07	42
lymphocyte	4.92e-07	53
common lymphoid progenitor	4.92e-07	53
lymphoid lineage restricted progenitor cell	5.41e-07	52
mature alpha-beta T cell	5.96e-07	18
alpha-beta T cell	5.96e-07	18
immature T cell	5.96e-07	18
mature T cell	5.96e-07	18
immature alpha-beta T cell	5.96e-07	18

Uber Anatomy

Ontology term	p-value	n
adult organism	3.95e-35	115
neural tube	9.40e-23	57
neural rod	9.40e-23	57
future spinal cord	9.40e-23	57
neural keel	9.40e-23	57
regional part of forebrain	2.02e-19	41
forebrain	2.02e-19	41
future forebrain	2.02e-19	41
anterior neural tube	3.41e-19	42
central nervous system	9.42e-19	82
regional part of brain	7.32e-18	59
brain	5.73e-17	69
future brain	5.73e-17	69
telencephalon	1.03e-16	34
gray matter	1.41e-16	34
brain grey matter	1.41e-16	34
regional part of nervous system	2.18e-16	94
nervous system	2.18e-16	94
regional part of telencephalon	4.32e-16	33
cerebral hemisphere	4.44e-16	32
regional part of cerebral cortex	1.28e-14	22
neocortex	1.81e-13	20
neural plate	4.49e-13	86
presumptive neural plate	4.49e-13	86
neurectoderm	4.81e-13	90
cerebral cortex	2.26e-12	25
pallium	2.26e-12	25
pre-chordal neural plate	2.62e-09	61
hematopoietic system	7.30e-07	102
blood island	7.30e-07	102

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
ATF3#467	2	14.9754496840058	0.00576829454079388	0.0259681414520441
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296414573092623
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190808088768417
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662363598335988
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.030692394242778
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.032703806390834
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323785766323667
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321985138749498
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464309514882876
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00764332772322354
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109030244272726
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128583515705889
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157409767057773
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.027050496122848
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0324896334244228
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381500951511986
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460692765632892
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173479458706404
PBX3#5090	2	14.6096751244961	0.00605612247321789	0.0268564126780351
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.008848015902657
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277883729849449
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457790816630379
SP2#6668	2	17.4356869958964	0.00427356848176974	0.0203273315419934
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330763545600327
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.03782413641868

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.