Coexpression cluster:C3712

Full id: C3712_granulocyte_Neutrophils_embryonic_non_Eosinophils_CD19_rectum

Phase1 CAGE Peaks

Hg19::chr18:2655849..2655941,+	p2@SMCHD1
Hg19::chr6:79787902..79787958,-	p1@PHIP
Hg19::chr6:79787964..79787994,-	p2@PHIP

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:0005158	insulin receptor binding	0.0263626274788933
GO:0008286	insulin receptor signaling pathway	0.0263626274788933

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	1.97e-39	172
angioblastic mesenchymal cell	1.97e-39	172
leukocyte	5.39e-36	140
hematopoietic oligopotent progenitor cell	6.35e-36	165
hematopoietic multipotent progenitor cell	6.35e-36	165
hematopoietic cell	2.06e-34	182
hematopoietic lineage restricted progenitor cell	3.37e-29	124
nongranular leukocyte	2.81e-28	119
myeloid cell	1.40e-18	112
common myeloid progenitor	1.40e-18	112
lymphocyte	8.84e-17	53
common lymphoid progenitor	8.84e-17	53
lymphoid lineage restricted progenitor cell	1.53e-16	52
myeloid leukocyte	2.13e-15	76
granulocyte monocyte progenitor cell	3.04e-13	71
myeloid lineage restricted progenitor cell	1.56e-12	70
classical monocyte	6.28e-12	45
CD14-positive, CD16-negative classical monocyte	1.16e-11	42
macrophage dendritic cell progenitor	4.00e-11	65
monopoietic cell	1.29e-10	63
monocyte	1.29e-10	63
monoblast	1.29e-10	63
promonocyte	1.29e-10	63
T cell	1.83e-09	25
pro-T cell	1.83e-09	25
mature alpha-beta T cell	2.57e-09	18
alpha-beta T cell	2.57e-09	18
immature T cell	2.57e-09	18
mature T cell	2.57e-09	18
immature alpha-beta T cell	2.57e-09	18
B cell	2.01e-07	14
lymphocyte of B lineage	5.52e-07	24
pro-B cell	5.52e-07	24

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	7.73e-16	102
blood island	7.73e-16	102
adult organism	1.02e-15	115
hemolymphoid system	4.04e-13	112
bone element	1.10e-09	86
bone marrow	1.17e-09	80
central nervous system	8.79e-09	82
neural tube	1.31e-08	57
neural rod	1.31e-08	57
future spinal cord	1.31e-08	57
neural keel	1.31e-08	57
regional part of nervous system	3.09e-08	94
nervous system	3.09e-08	94
anterior neural tube	1.87e-07	42
brain	3.44e-07	69
future brain	3.44e-07	69
regional part of forebrain	4.27e-07	41
forebrain	4.27e-07	41
future forebrain	4.27e-07	41
regional part of brain	5.47e-07	59
skeletal element	7.80e-07	101
skeletal system	7.80e-07	101

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	0.01898989744589
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320452284945039
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.046193112376064
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00387741001519902
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00391151392763827
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.026944361457064
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381242923672077
PBX3#5090	2	14.6096751244961	0.00605612247321789	0.0268279341270955
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00881755219067387
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.0298273043645913
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276498269657892
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00615649363831036
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329059296887961
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329121273170983

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.