Coexpression cluster:C1165

Full id: C1165_occipital_parietal_duodenum_temporal_brain_medial_frontal

Phase1 CAGE Peaks

Hg19::chr12:122459956..122459988,+	p3@BCL7A
Hg19::chr5:88036490..88036495,-	p@chr5:88036490..88036495 -
Hg19::chr5:88178983..88179012,-	p1@MEF2C
Hg19::chr5:88179017..88179046,-	p2@MEF2C
Hg19::chr5:88179195..88179224,-	p3@MEF2C
Hg19::chr5:88179518..88179569,-	p5@MEF2C
Hg19::chr6:62996066..62996137,-	p1@KHDRBS2

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:0001958	endochondral ossification	0.015700393513282
GO:0001974	blood vessel remodeling	0.015700393513282
GO:0002062	chondrocyte differentiation	0.015700393513282
GO:0045449	regulation of transcription	0.015700393513282
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.015700393513282
GO:0006350	transcription	0.015700393513282
GO:0010468	regulation of gene expression	0.015700393513282
GO:0031323	regulation of cellular metabolic process	0.015700393513282
GO:0019222	regulation of metabolic process	0.0163963732111183
GO:0001649	osteoblast differentiation	0.0178697429430301
GO:0051216	cartilage development	0.0233855421719481
GO:0010467	gene expression	0.0279180613752491
GO:0050794	regulation of cellular process	0.0294799521563611
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0295006278096016
GO:0050789	regulation of biological process	0.0318685023796382
GO:0031214	biomineral formation	0.034238230533469
GO:0001503	ossification	0.034238230533469
GO:0065007	biological regulation	0.034238230533469
GO:0007507	heart development	0.034238230533469
GO:0046849	bone remodeling	0.034238230533469
GO:0048771	tissue remodeling	0.0356553666608488
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.045010292622195
GO:0048514	blood vessel morphogenesis	0.0455204763418833
GO:0001568	blood vessel development	0.0470817168598508
GO:0001944	vasculature development	0.0470817168598508
GO:0007517	muscle development	0.0470817168598508
GO:0003713	transcription coactivator activity	0.0492700420420545

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	1.04e-14	172
angioblastic mesenchymal cell	1.04e-14	172
myeloid cell	1.28e-14	112
common myeloid progenitor	1.28e-14	112
hematopoietic cell	2.39e-13	182
hematopoietic oligopotent progenitor cell	3.59e-13	165
hematopoietic multipotent progenitor cell	3.59e-13	165
lymphocyte of B lineage	4.19e-12	24
pro-B cell	4.19e-12	24
CD14-positive, CD16-negative classical monocyte	2.50e-11	42
monopoietic cell	5.04e-10	63
monocyte	5.04e-10	63
monoblast	5.04e-10	63
promonocyte	5.04e-10	63
macrophage dendritic cell progenitor	5.17e-10	65
B cell	2.69e-09	14
leukocyte	3.82e-09	140
myeloid leukocyte	4.04e-09	76
nongranular leukocyte	5.38e-09	119
classical monocyte	5.55e-09	45
granulocyte monocyte progenitor cell	3.57e-08	71
myeloid lineage restricted progenitor cell	2.66e-07	70

Uber Anatomy

Ontology term	p-value	n
adult organism	1.23e-40	115
neural tube	9.05e-24	57
neural rod	9.05e-24	57
future spinal cord	9.05e-24	57
neural keel	9.05e-24	57
anterior neural tube	5.03e-22	42
regional part of forebrain	7.51e-22	41
forebrain	7.51e-22	41
future forebrain	7.51e-22	41
central nervous system	1.18e-20	82
regional part of brain	2.42e-20	59
telencephalon	1.32e-18	34
gray matter	3.44e-18	34
brain grey matter	3.44e-18	34
cerebral hemisphere	5.43e-18	32
regional part of telencephalon	5.46e-18	33
brain	1.10e-17	69
future brain	1.10e-17	69
regional part of nervous system	5.42e-16	94
nervous system	5.42e-16	94
regional part of cerebral cortex	9.84e-16	22
cerebral cortex	6.51e-15	25
pallium	6.51e-15	25
neocortex	1.15e-14	20
neural plate	1.86e-12	86
presumptive neural plate	1.86e-12	86
neurectoderm	9.98e-12	90
hemolymphoid system	2.76e-11	112
pre-chordal neural plate	2.11e-10	61
hematopoietic system	2.54e-10	102
blood island	2.54e-10	102
tissue	3.98e-10	787
bone element	7.31e-08	86
bone marrow	1.21e-07	80
tube	7.97e-07	194

Disease

Ontology term	p-value	n
myeloid leukemia	3.40e-08	31

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)
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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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No analysis results for this cluster

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.