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Coexpression cluster:C2513

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Full id: C2513_cord_mycosis_CD4_thymus_NK_chronic_CD8



Phase1 CAGE Peaks

Hg19::chr1:111415703..111415714,+p4@CD53
Hg19::chr2:181988620..181988686,+p1@ENST00000424655
p1@ENST00000428474
Hg19::chr6:149461279..149461299,+p@chr6:149461279..149461299
+
Hg19::chr6:149461322..149461343,+p@chr6:149461322..149461343
+


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 cell5.56e-46172
angioblastic mesenchymal cell5.56e-46172
hematopoietic cell1.90e-45182
hematopoietic oligopotent progenitor cell1.05e-41165
hematopoietic multipotent progenitor cell1.05e-41165
leukocyte3.02e-38140
lymphocyte1.12e-3453
common lymphoid progenitor1.12e-3453
lymphoid lineage restricted progenitor cell3.55e-3452
nongranular leukocyte6.97e-32119
hematopoietic lineage restricted progenitor cell5.67e-30124
T cell5.38e-2125
pro-T cell5.38e-2125
mature alpha-beta T cell1.29e-1518
alpha-beta T cell1.29e-1518
immature T cell1.29e-1518
mature T cell1.29e-1518
immature alpha-beta T cell1.29e-1518
myeloid cell7.37e-13112
common myeloid progenitor7.37e-13112
lymphocyte of B lineage2.50e-1224
pro-B cell2.50e-1224
CD8-positive, alpha-beta T cell2.27e-1011
B cell6.32e-0714
mesenchymal cell6.56e-07358
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.37e-13102
blood island3.37e-13102
adult organism1.06e-12115
blood1.68e-1215
haemolymphatic fluid1.68e-1215
organism substance1.68e-1215
hemolymphoid system1.65e-11112
Disease
Ontology termp-valuen
hematologic cancer8.99e-1551
immune system cancer8.99e-1551
leukemia6.28e-1139
lymphoma4.39e-0710


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
BATF#10538318.26835134422770.0002681660105721290.00286692496449407
BCL11A#53335321.27709132770530.0001704839114606140.0020815021310539
GATA2#262439.55869880016550.001818151618357440.0108998299104318
PAX5#507935.002174148383370.01196533174786410.043496250693184



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.