Coexpression cluster:C2977

Full id: C2977_CD14_Dendritic_serous_Smooth_Basophils_cerebellum_CD34

Phase1 CAGE Peaks

Hg19::chr10:112257429..112257447,-	p@chr10:112257429..112257447 -
Hg19::chr10:112257453..112257476,-	p@chr10:112257453..112257476 -
Hg19::chr10:112257490..112257512,-	p@chr10:112257490..112257512 -

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
classical monocyte	4.08e-21	42
CD14-positive, CD16-negative classical monocyte	4.08e-21	42
leukocyte	7.99e-16	136
defensive cell	8.18e-15	48
phagocyte	8.18e-15	48
nongranular leukocyte	2.87e-11	115
myeloid leukocyte	4.53e-11	72
hematopoietic lineage restricted progenitor cell	1.31e-10	120
connective tissue cell	1.60e-10	361
granulocyte monocyte progenitor cell	3.90e-10	67
macrophage dendritic cell progenitor	6.00e-10	61
mesenchymal cell	8.96e-10	354
somatic cell	2.56e-09	588
monopoietic cell	3.06e-09	59
monocyte	3.06e-09	59
monoblast	3.06e-09	59
promonocyte	3.06e-09	59
native cell	4.05e-09	722
myeloid lineage restricted progenitor cell	1.81e-08	66
multi fate stem cell	2.40e-08	427
somatic stem cell	6.68e-08	433
motile cell	7.21e-08	386
hematopoietic stem cell	1.03e-07	168
angioblastic mesenchymal cell	1.03e-07	168
stem cell	1.67e-07	441
hematopoietic cell	2.45e-07	177
animal cell	2.63e-07	679
eukaryotic cell	2.63e-07	679

Uber Anatomy

Ontology term	p-value	n
bone marrow	5.66e-11	76
immune system	1.93e-10	93
skeletal system	7.12e-10	100
bone element	9.65e-10	82
connective tissue	2.29e-09	371
skeletal element	7.81e-09	90
hemolymphoid system	3.43e-08	108
hematopoietic system	4.37e-08	98
blood island	4.37e-08	98

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	0.0189015886083728
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323328521288084
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320187589488892
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0318861438752535
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0459733171229407
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255042959119962
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153603092524158
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127548131575069
MEF2A#4205	3	18.7432309096441	0.000151824390562247	0.00194724149894762
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268424772675038
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172181099503641
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00879176659621926
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245309888557446
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0108776197715627
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00373786260511044
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00540258189138205
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00611399496469482
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00612684027880757
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189403424099401
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327726535981232
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00387537937282365
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0108871450076587

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.