Coexpression cluster:C3902

Full id: C3902_Hepatocyte_liver_hepatoma_Neutrophils_medulla_placenta_CD4

Phase1 CAGE Peaks

Hg19::chr1:169555677..169555678,-	p4@F5
Hg19::chr1:169555684..169555705,-	p2@F5
Hg19::chr1:169555709..169555730,-	p1@F5

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
CD14-positive, CD16-negative classical monocyte	2.87e-25	42
leukocyte	4.29e-24	140
classical monocyte	3.10e-22	45
myeloid leukocyte	2.26e-21	76
hematopoietic lineage restricted progenitor cell	9.72e-20	124
nongranular leukocyte	2.79e-19	119
hematopoietic stem cell	2.99e-17	172
angioblastic mesenchymal cell	2.99e-17	172
myeloid lineage restricted progenitor cell	9.22e-17	70
hematopoietic cell	2.35e-16	182
granulocyte monocyte progenitor cell	1.09e-15	71
hematopoietic oligopotent progenitor cell	1.83e-15	165
hematopoietic multipotent progenitor cell	1.83e-15	165
monopoietic cell	3.67e-15	63
monocyte	3.67e-15	63
monoblast	3.67e-15	63
promonocyte	3.67e-15	63
macrophage dendritic cell progenitor	8.76e-15	65
myeloid cell	2.51e-11	112
common myeloid progenitor	2.51e-11	112
granulocyte	5.86e-07	8

Uber Anatomy

Ontology term	p-value	n
adult organism	1.87e-37	115
hematopoietic system	5.42e-21	102
blood island	5.42e-21	102
hemolymphoid system	3.57e-18	112
immune system	5.59e-15	115
bone marrow	3.64e-12	80
neural tube	1.04e-10	57
neural rod	1.04e-10	57
future spinal cord	1.04e-10	57
neural keel	1.04e-10	57
bone element	5.20e-10	86
blood	6.82e-10	15
haemolymphatic fluid	6.82e-10	15
organism substance	6.82e-10	15
regional part of brain	7.65e-08	59
anterior neural tube	1.10e-07	42
regional part of forebrain	2.08e-07	41
forebrain	2.08e-07	41
future forebrain	2.08e-07	41

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279559337806528
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167531556073771
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.0066426332253927
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276962426565157
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.0030918087231846
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.0064281321617488
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00614139788114202
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389244369810532

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.