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Coexpression cluster:C1919

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Full id: C1919_immature_CD4_Dendritic_Peripheral_Natural_migratory_CD8



Phase1 CAGE Peaks

Hg19::chr3:135913298..135913322,-p7@MSL2
Hg19::chr3:16553385..16553420,-p@chr3:16553385..16553420
-
Hg19::chr3:16553696..16553720,+p@chr3:16553696..16553720
+
Hg19::chr3:16553730..16553747,+p@chr3:16553730..16553747
+
Hg19::chr3:16553761..16553777,+p@chr3:16553761..16553777
+


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
leukocyte8.43e-64140
hematopoietic stem cell8.53e-63172
angioblastic mesenchymal cell8.53e-63172
hematopoietic cell1.18e-60182
hematopoietic oligopotent progenitor cell1.26e-56165
hematopoietic multipotent progenitor cell1.26e-56165
nongranular leukocyte4.55e-51119
hematopoietic lineage restricted progenitor cell1.64e-50124
lymphocyte6.50e-3453
common lymphoid progenitor6.50e-3453
lymphoid lineage restricted progenitor cell8.91e-3452
mesenchymal cell3.72e-27358
connective tissue cell1.69e-25365
myeloid cell1.86e-23112
common myeloid progenitor1.86e-23112
CD14-positive, CD16-negative classical monocyte2.55e-2342
motile cell2.36e-22390
classical monocyte1.15e-2045
myeloid leukocyte3.83e-2076
granulocyte monocyte progenitor cell1.54e-1971
macrophage dendritic cell progenitor2.20e-1765
lymphocyte of B lineage7.83e-1724
pro-B cell7.83e-1724
multi fate stem cell1.24e-16430
myeloid lineage restricted progenitor cell1.68e-1670
stem cell1.69e-16444
somatic stem cell5.27e-16436
monopoietic cell6.91e-1663
monocyte6.91e-1663
monoblast6.91e-1663
promonocyte6.91e-1663
T cell2.97e-1525
pro-T cell2.97e-1525
mature alpha-beta T cell1.47e-1218
alpha-beta T cell1.47e-1218
immature T cell1.47e-1218
mature T cell1.47e-1218
immature alpha-beta T cell1.47e-1218
B cell1.79e-1114
dendritic cell3.05e-0810
intermediate monocyte3.14e-079
CD14-positive, CD16-positive monocyte3.14e-079
CD4-positive, alpha-beta T cell3.26e-076
CD8-positive, alpha-beta T cell6.78e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.72e-24102
blood island1.72e-24102
connective tissue3.37e-24375
hemolymphoid system1.13e-20112
bone marrow1.14e-1780
bone element2.92e-1686
immune system5.62e-14115
skeletal element1.16e-11101
skeletal system1.16e-11101
Disease
Ontology termp-valuen
hematologic cancer1.45e-0851
immune system cancer1.45e-0851


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.