Coexpression cluster:C1181

Full id: C1181_Myoblast_CD14_liposarcoma_mesenchymal_caudate_diencephalon_putamen

Phase1 CAGE Peaks

Hg19::chr12:90102690..90102701,-	p13@ATP2B1
Hg19::chr12:90102773..90102784,-	p6@ATP2B1
Hg19::chr12:90102800..90102814,-	p4@ATP2B1
Hg19::chr12:90102818..90102829,-	p10@ATP2B1
Hg19::chr12:90102935..90102948,-	p5@ATP2B1
Hg19::chr12:90102960..90102971,-	p7@ATP2B1
Hg19::chr12:90102986..90102998,-	p12@ATP2B1

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	3.85e-25	42
leukocyte	1.07e-23	140
classical monocyte	1.23e-23	45
nongranular leukocyte	1.76e-20	119
myeloid leukocyte	2.18e-20	76
macrophage dendritic cell progenitor	6.82e-19	65
monopoietic cell	2.55e-18	63
monocyte	2.55e-18	63
monoblast	2.55e-18	63
promonocyte	2.55e-18	63
hematopoietic lineage restricted progenitor cell	6.51e-18	124
granulocyte monocyte progenitor cell	7.95e-18	71
myeloid lineage restricted progenitor cell	2.59e-15	70
hematopoietic stem cell	3.03e-14	172
angioblastic mesenchymal cell	3.03e-14	172
hematopoietic oligopotent progenitor cell	2.81e-13	165
hematopoietic multipotent progenitor cell	2.81e-13	165
hematopoietic cell	1.17e-11	182
connective tissue cell	2.97e-10	365
myeloid cell	4.29e-10	112
common myeloid progenitor	4.29e-10	112
mesenchymal cell	6.06e-10	358
multi fate stem cell	4.32e-09	430
stem cell	1.71e-08	444
somatic stem cell	3.44e-08	436
motile cell	2.92e-07	390

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.60e-16	102
blood island	2.60e-16	102
bone marrow	1.98e-15	80
bone element	2.66e-13	86
cerebral hemisphere	3.10e-13	32
regional part of forebrain	8.86e-13	41
forebrain	8.86e-13	41
future forebrain	8.86e-13	41
hemolymphoid system	1.49e-12	112
telencephalon	3.94e-12	34
skeletal element	4.82e-12	101
skeletal system	4.82e-12	101
regional part of cerebral cortex	4.94e-12	22
anterior neural tube	7.76e-12	42
regional part of telencephalon	1.41e-11	33
gray matter	3.60e-11	34
brain grey matter	3.60e-11	34
neocortex	4.68e-11	20
connective tissue	5.49e-11	375
cerebral cortex	1.37e-09	25
pallium	1.37e-09	25
neural tube	2.62e-09	57
neural rod	2.62e-09	57
future spinal cord	2.62e-09	57
neural keel	2.62e-09	57
immune system	6.61e-09	115
central nervous system	9.96e-09	82
regional part of brain	1.01e-08	59
brain	3.06e-08	69
future brain	3.06e-08	69
musculoskeletal system	5.23e-08	167
regional part of nervous system	5.73e-08	94
nervous system	5.73e-08	94

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
ATF3#467	6	19.2541495937218	5.23155102976118e-08	3.33360560095929e-06
BHLHE40#8553	7	44.8718135469774	2.71655591272133e-12	3.64203315749298e-10
CCNT2#905	7	6.33620157696263	2.43743907326287e-06	8.61759307286733e-05
CHD2#1106	7	10.3440228341169	7.88338195961115e-08	4.72094339724673e-06
CTCF#10664	7	5.36025637307503	7.86114662284756e-06	0.00022237548541267
E2F1#1869	7	4.90738921487932	1.45832274679793e-05	0.000346779984865276
E2F6#1876	7	5.01715573169739	1.24910426162553e-05	0.000308113367926095
EGR1#1958	7	4.98817909481014	1.30079520165561e-05	0.000318084172478834
GATA1#2623	3	5.81156063305733	0.0111931160082029	0.0411271405425239
HDAC2#3066	6	11.4991030599654	1.1228817392662e-06	4.62067162991419e-05
HEY1#23462	7	4.04011104310571	5.68979821988558e-05	0.00094986706567556
JUND#3727	6	5.99542623588945	5.24232039014691e-05	0.000891262736816789
MAX#4149	6	5.53076186486325	8.40673768319711e-05	0.00126184431861946
NFKB1#4790	7	5.48806342419384	6.66568321176054e-06	0.000194674857089782
NRF1#4899	5	8.72162817693636	6.71450045004423e-05	0.00107356967621275
PAX5#5079	7	6.66956553117783	1.7023051190758e-06	6.43456548429814e-05
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223330512094392
SIN3A#25942	7	5.40888472681514	7.3795239773719e-06	0.000211559183275527
TAF1#6872	7	3.34304628574529	0.000214233631962245	0.00246522105426454
TBP#6908	6	3.17723201751119	0.00207411205185266	0.012018986216692
TFAP2C#7022	7	10.8092286098602	5.79365976833206e-08	3.61028659036296e-06
USF1#7391	6	5.45271366617825	9.13505145927422e-05	0.00133136427484669
USF2#7392	7	12.9921973850696	1.59819543071901e-08	1.16641462326249e-06

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.