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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
lymphocyte1.61e-4353
common lymphoid progenitor1.61e-4353
lymphoid lineage restricted progenitor cell9.37e-4352
nucleate cell2.68e-4155
hematopoietic cell8.87e-36177
hematopoietic stem cell4.66e-35168
angioblastic mesenchymal cell4.66e-35168
T cell2.44e-3125
pro-T cell2.44e-3125
hematopoietic oligopotent progenitor cell9.37e-31161
hematopoietic multipotent progenitor cell9.37e-31161
leukocyte1.58e-30136
nongranular leukocyte1.07e-29115
hematopoietic lineage restricted progenitor cell3.88e-23120
mature alpha-beta T cell6.64e-2318
alpha-beta T cell6.64e-2318
immature T cell6.64e-2318
mature T cell6.64e-2318
immature alpha-beta T cell6.64e-2318
CD8-positive, alpha-beta T cell6.80e-1511
lymphocyte of B lineage3.02e-1124
pro-B cell3.02e-1124
circulating cell1.05e-086
CD4-positive, alpha-beta T cell2.93e-086
Uber Anatomy
Ontology termp-valuen
blood1.57e-1815
haemolymphatic fluid1.57e-1815
organism substance1.57e-1815
hemopoietic organ2.11e-097
immune organ2.11e-097
hematopoietic system2.30e-0998
blood island2.30e-0998
hemolymphoid system8.60e-09108
adult organism1.57e-08114
Disease
Ontology termp-valuen
hematologic cancer2.46e-1451
immune system cancer2.46e-1451
lymphoma2.87e-1010
leukemia1.40e-0839


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.