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Coexpression cluster:C1822

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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


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


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>


Cell Type
Ontology termp-valuen
somatic cell1.39e-34588
multi fate stem cell7.63e-33427
somatic stem cell3.49e-32433
stem cell1.57e-30441
mesenchymal cell2.49e-27354
connective tissue cell6.62e-27361
myeloid leukocyte1.70e-2472
native cell4.75e-24722
defensive cell6.32e-2448
phagocyte6.32e-2448
myeloid cell4.51e-23108
common myeloid progenitor4.51e-23108
hematopoietic stem cell2.74e-22168
angioblastic mesenchymal cell2.74e-22168
classical monocyte4.46e-2242
CD14-positive, CD16-negative classical monocyte4.46e-2242
hematopoietic cell5.37e-22177
macrophage dendritic cell progenitor8.68e-2261
hematopoietic oligopotent progenitor cell1.19e-21161
hematopoietic multipotent progenitor cell1.19e-21161
monopoietic cell1.38e-2159
monocyte1.38e-2159
monoblast1.38e-2159
promonocyte1.38e-2159
granulocyte monocyte progenitor cell3.43e-2167
leukocyte3.50e-20136
motile cell5.53e-20386
myeloid lineage restricted progenitor cell1.07e-1966
nongranular leukocyte7.78e-19115
animal cell2.64e-17679
eukaryotic cell2.64e-17679
hematopoietic lineage restricted progenitor cell3.24e-17120
stuff accumulating cell2.15e-0987
mesodermal cell2.41e-08121
endothelial cell3.27e-0736
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm3.32e-34203
connective tissue4.59e-25371
hematopoietic system4.35e-2198
blood island4.35e-2198
hemolymphoid system1.51e-20108
mesoderm7.43e-20315
mesoderm-derived structure7.43e-20315
presumptive mesoderm7.43e-20315
bone marrow6.58e-1976
bone element2.54e-1882
immune system1.78e-1793
skeletal element1.12e-1590
musculoskeletal system1.45e-15167
cardiovascular system4.07e-14109
skeletal system1.85e-13100
circulatory system2.23e-13112
epithelial tube open at both ends1.30e-1159
blood vessel1.30e-1159
blood vasculature1.30e-1159
vascular cord1.30e-1159
splanchnic layer of lateral plate mesoderm2.37e-1183
artery3.76e-1142
arterial blood vessel3.76e-1142
arterial system3.76e-1142
vasculature6.55e-1178
vascular system6.55e-1178
vessel1.29e-1068
systemic artery1.74e-0833
systemic arterial system1.74e-0833


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


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCFL#140690311.84788461538460.001201770348538230.00815169795615926
EBF1#187947.12517347725520.0007230531046774210.00577110761936608
GTF2B#2959212.77753197372970.00919936089559720.0347891535132446
NFKB1#479055.488063424193840.0002008162847462320.00239118138896496
RAD21#588536.21302033727380.007751055068811640.0318956832281962
SIN3A#2594244.327107781452110.004977052855762880.0232447197568652
SMC3#912639.02695970695970.002650964449467550.0146395979345358
ZNF143#770238.100525931336740.003624870512090980.018333067865001



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


This analysis result is provided for C0 - C305 clusters.