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Coexpression cluster:C4156

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Full id: C4156_acute_chronic_Reticulocytes_thymus_CD4_CD34_CD8



Phase1 CAGE Peaks

Hg19::chr2:182322766..182322767,+p22@ITGA4
Hg19::chr2:182322842..182322860,+p7@ITGA4
Hg19::chr2:182322864..182322885,+p3@ITGA4


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell2.62e-66172
angioblastic mesenchymal cell2.62e-66172
hematopoietic cell1.04e-63182
hematopoietic oligopotent progenitor cell1.61e-61165
hematopoietic multipotent progenitor cell1.61e-61165
leukocyte5.58e-49140
hematopoietic lineage restricted progenitor cell7.01e-42124
nongranular leukocyte6.67e-41119
myeloid cell2.65e-33112
common myeloid progenitor2.65e-33112
lymphocyte2.47e-2553
common lymphoid progenitor2.47e-2553
lymphoid lineage restricted progenitor cell6.60e-2552
mesenchymal cell9.15e-22358
connective tissue cell2.12e-20365
myeloid leukocyte4.11e-1976
motile cell1.01e-18390
CD14-positive, CD16-negative classical monocyte1.50e-1842
myeloid lineage restricted progenitor cell1.52e-1770
granulocyte monocyte progenitor cell1.62e-1671
classical monocyte4.30e-1645
multi fate stem cell1.64e-14430
monopoietic cell1.96e-1463
monocyte1.96e-1463
monoblast1.96e-1463
promonocyte1.96e-1463
stem cell2.84e-14444
macrophage dendritic cell progenitor4.01e-1465
somatic stem cell1.08e-13436
T cell1.57e-1225
pro-T cell1.57e-1225
mature alpha-beta T cell3.82e-1218
alpha-beta T cell3.82e-1218
immature T cell3.82e-1218
mature T cell3.82e-1218
immature alpha-beta T cell3.82e-1218
lymphocyte of B lineage6.32e-1224
pro-B cell6.32e-1224
B cell1.49e-0914
CD8-positive, alpha-beta T cell2.69e-0911
intermediate monocyte8.19e-079
CD14-positive, CD16-positive monocyte8.19e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.95e-25102
blood island2.95e-25102
hemolymphoid system3.69e-22112
connective tissue1.48e-19375
bone marrow1.82e-1480
bone element2.60e-1486
immune system8.71e-11115
blood1.15e-0915
haemolymphatic fluid1.15e-0915
organism substance1.15e-0915
skeletal element1.17e-09101
skeletal system1.17e-09101
Disease
Ontology termp-valuen
hematologic cancer2.58e-1551
immune system cancer2.58e-1551
leukemia4.86e-1439
myeloid leukemia5.13e-1331


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


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


This analysis result is provided for C0 - C305 clusters.