Coexpression cluster:C4532

Full id: C4532_Mast_CD14_Eosinophils_caudate_putamen_Endothelial_diencephalon

Phase1 CAGE Peaks

Hg19::chr5:94417266..94417281,-	p3@MCTP1
Hg19::chr5:94417287..94417295,-	p4@MCTP1
Hg19::chr5:94417314..94417337,-	p2@MCTP1

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
myeloid leukocyte	8.21e-36	76
granulocyte monocyte progenitor cell	8.21e-33	71
myeloid lineage restricted progenitor cell	2.92e-30	70
macrophage dendritic cell progenitor	1.40e-29	65
myeloid cell	9.00e-29	112
common myeloid progenitor	9.00e-29	112
monopoietic cell	2.35e-28	63
monocyte	2.35e-28	63
monoblast	2.35e-28	63
promonocyte	2.35e-28	63
CD14-positive, CD16-negative classical monocyte	1.84e-27	42
classical monocyte	2.70e-27	45
leukocyte	4.04e-20	140
hematopoietic stem cell	9.78e-20	172
angioblastic mesenchymal cell	9.78e-20	172
hematopoietic oligopotent progenitor cell	1.76e-17	165
hematopoietic multipotent progenitor cell	1.76e-17	165
hematopoietic cell	2.12e-16	182
hematopoietic lineage restricted progenitor cell	1.39e-15	124
nongranular leukocyte	2.42e-14	119

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	5.19e-34	112
hematopoietic system	7.96e-32	102
blood island	7.96e-32	102
bone marrow	5.74e-30	80
bone element	1.81e-26	86
immune system	1.73e-24	115
skeletal element	6.05e-19	101
skeletal system	6.05e-19	101
adult organism	2.00e-13	115
anterior neural tube	1.19e-08	42
lateral plate mesoderm	1.52e-08	216
regional part of forebrain	2.02e-08	41
forebrain	2.02e-08	41
future forebrain	2.02e-08	41
regional part of brain	7.49e-08	59
neural tube	1.15e-07	57
neural rod	1.15e-07	57
future spinal cord	1.15e-07	57
neural keel	1.15e-07	57
pre-chordal neural plate	3.91e-07	61
embryonic structure	5.32e-07	605
developing anatomical structure	5.32e-07	605
cerebral hemisphere	5.35e-07	32
organ	6.56e-07	511
germ layer	6.59e-07	604
embryonic tissue	6.59e-07	604
presumptive structure	6.59e-07	604
epiblast (generic)	6.59e-07	604
musculoskeletal system	7.24e-07	167
neural plate	8.39e-07	86
presumptive neural plate	8.39e-07	86

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
BATF#10538	3	24.3578017923036	6.91705216281876e-05	0.00110207476862338
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164486332299403
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115663705748503
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168219398432976
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00901128129200808
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435697869406815
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00446049887092089
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157499135183587
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187268371603245
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270655608724345
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00885198032122697
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00667800903252928
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00486399038977351
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109354928353484
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00645031885505173
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00631596808040091
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00422705299068011

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.