Coexpression cluster:C1822

Full id: C1822_CD14_CD8_Neutrophils_Natural_Renal_Endothelial_acute

Phase1 CAGE Peaks

Hg19::chr19:41858620..41858632,-	p13@TGFB1
Hg19::chr19:41858640..41858665,-	p6@TGFB1
Hg19::chr19:41859298..41859309,-	p4@TGFB1
Hg19::chr19:41859532..41859555,+	p@chr19:41859532..41859555 +
Hg19::chr19:41859814..41859837,-	p1@TGFB1

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
somatic cell	2.65e-35	591
multi fate stem cell	4.77e-33	430
somatic stem cell	2.80e-32	436
stem cell	5.05e-30	444
mesenchymal cell	7.81e-28	358
connective tissue cell	9.32e-28	365
native cell	2.90e-24	722
CD14-positive, CD16-negative classical monocyte	2.66e-22	42
myeloid leukocyte	3.07e-22	76
myeloid cell	3.01e-21	112
common myeloid progenitor	3.01e-21	112
hematopoietic cell	3.50e-21	182
hematopoietic stem cell	6.02e-21	172
angioblastic mesenchymal cell	6.02e-21	172
hematopoietic oligopotent progenitor cell	1.61e-20	165
hematopoietic multipotent progenitor cell	1.61e-20	165
motile cell	3.38e-20	390
leukocyte	1.28e-18	140
granulocyte monocyte progenitor cell	1.67e-18	71
classical monocyte	2.65e-18	45
macrophage dendritic cell progenitor	3.98e-18	65
monopoietic cell	5.54e-18	63
monocyte	5.54e-18	63
monoblast	5.54e-18	63
promonocyte	5.54e-18	63
myeloid lineage restricted progenitor cell	2.93e-17	70
animal cell	3.36e-17	679
eukaryotic cell	3.36e-17	679
nongranular leukocyte	7.78e-17	119
hematopoietic lineage restricted progenitor cell	7.06e-16	124
mesodermal cell	7.63e-09	119
endothelial cell	2.03e-07	35
vascular associated smooth muscle cell	7.53e-07	32

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	1.41e-33	216
connective tissue	1.28e-25	375
hematopoietic system	1.40e-19	102
blood island	1.40e-19	102
hemolymphoid system	9.11e-19	112
bone marrow	6.02e-17	80
bone element	3.04e-16	86
musculoskeletal system	1.58e-15	167
cardiovascular system	4.08e-15	110
circulatory system	4.14e-14	113
blood vessel	6.61e-13	60
epithelial tube open at both ends	6.61e-13	60
blood vasculature	6.61e-13	60
vascular cord	6.61e-13	60
immune system	1.12e-12	115
splanchnic layer of lateral plate mesoderm	1.44e-12	84
artery	1.52e-12	42
arterial blood vessel	1.52e-12	42
arterial system	1.52e-12	42
skeletal element	1.98e-12	101
skeletal system	1.98e-12	101
vessel	1.04e-11	69
vasculature	1.26e-11	79
vascular system	1.26e-11	79
systemic artery	1.17e-09	33
systemic arterial system	1.17e-09	33
epithelial tube	9.27e-08	118

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
CTCFL#140690	3	11.8478846153846	0.00120177034853823	0.00815169795615926
EBF1#1879	4	7.1251734772552	0.000723053104677421	0.00577110761936608
GTF2B#2959	2	12.7775319737297	0.0091993608955972	0.0347891535132446
NFKB1#4790	5	5.48806342419384	0.000200816284746232	0.00239118138896496
RAD21#5885	3	6.2130203372738	0.00775105506881164	0.0318956832281962
SIN3A#25942	4	4.32710778145211	0.00497705285576288	0.0232447197568652
SMC3#9126	3	9.0269597069597	0.00265096444946755	0.0146395979345358
ZNF143#7702	3	8.10052593133674	0.00362487051209098	0.018333067865001

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.