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Coexpression cluster:C487: Difference between revisions

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|full_id=C487_CD4_Peripheral_CD8_Natural_CD14_immature_Basophils
|full_id=C487_CD4_Peripheral_CD8_Natural_CD14_immature_Basophils
|id=C487
|id=C487
|ontology_enrichment_celltype=CL:0000738!1.04e-28!140;CL:0000988!3.05e-20!182;CL:0000037!3.93e-20!172;CL:0000566!3.93e-20!172;CL:0002031!2.43e-19!124;CL:0002087!1.96e-18!119;CL:0002032!4.41e-17!165;CL:0000837!4.41e-17!165;CL:0000791!8.06e-17!18;CL:0000789!8.06e-17!18;CL:0002420!8.06e-17!18;CL:0002419!8.06e-17!18;CL:0000790!8.06e-17!18;CL:0002057!6.98e-14!42;CL:0000766!1.08e-13!76;CL:0000860!1.93e-12!45;CL:0000084!5.66e-12!25;CL:0000827!5.66e-12!25;CL:0000557!3.34e-11!71;CL:0000624!3.78e-10!6;CL:0000625!5.54e-10!11;CL:0002009!1.40e-09!65;CL:0000839!1.55e-09!70;CL:0000763!3.82e-09!112;CL:0000049!3.82e-09!112;CL:0000838!6.57e-09!52;CL:0000542!1.30e-08!53;CL:0000051!1.30e-08!53;CL:0000080!2.31e-08!6;CL:0002194!3.08e-08!63;CL:0000576!3.08e-08!63;CL:0000040!3.08e-08!63;CL:0000559!3.08e-08!63
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.17e-16!102;UBERON:0003061!1.17e-16!102;UBERON:0002193!8.81e-15!112;UBERON:0002371!6.23e-09!80;UBERON:0002405!7.87e-08!115;UBERON:0001474!1.03e-07!86;UBERON:0000178!2.08e-07!15;UBERON:0000179!2.08e-07!15;UBERON:0000463!2.08e-07!15
}}
}}

Revision as of 14:53, 21 May 2012


Full id: C487_CD4_Peripheral_CD8_Natural_CD14_immature_Basophils



Phase1 CAGE Peaks

Hg19::chr10:116285481..116285484,-p@chr10:116285481..116285484
-
Hg19::chr10:116301431..116301440,+p@chr10:116301431..116301440
+
Hg19::chr10:22053811..22053858,-p@chr10:22053811..22053858
-
Hg19::chr12:52980179..52980184,+p@chr12:52980179..52980184
+
Hg19::chr12:53039248..53039257,-p@chr12:53039248..53039257
-
Hg19::chr12:53039641..53039647,+p@chr12:53039641..53039647
+
Hg19::chr12:53039683..53039695,+p@chr12:53039683..53039695
+
Hg19::chr13:100024364..100024401,-p@chr13:100024364..100024401
-
Hg19::chr16:22546145..22546152,+p@chr16:22546145..22546152
+
Hg19::chr17:2166589..2166595,-p@chr17:2166589..2166595
-
Hg19::chr17:44342424..44342435,+p@chr17:44342424..44342435
+
Hg19::chr17:80085902..80085908,+p@chr17:80085902..80085908
+
Hg19::chr20:1267390..1267394,-p@chr20:1267390..1267394
-
Hg19::chr2:238616388..238616397,+p@chr2:238616388..238616397
+
Hg19::chr3:59996534..59996538,-p@chr3:59996534..59996538
-
Hg19::chr3:71527852..71527877,-p@chr3:71527852..71527877
-
Hg19::chr5:141484393..141484402,+p@chr5:141484393..141484402
+
Hg19::chr6:90981633..90981642,-p@chr6:90981633..90981642
-
Hg19::chr7:3501786..3501792,+p@chr7:3501786..3501792
+


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
leukocyte1.04e-28140
hematopoietic cell3.05e-20182
hematopoietic stem cell3.93e-20172
angioblastic mesenchymal cell3.93e-20172
hematopoietic lineage restricted progenitor cell2.43e-19124
nongranular leukocyte1.96e-18119
hematopoietic oligopotent progenitor cell4.41e-17165
hematopoietic multipotent progenitor cell4.41e-17165
mature alpha-beta T cell8.06e-1718
alpha-beta T cell8.06e-1718
immature T cell8.06e-1718
mature T cell8.06e-1718
immature alpha-beta T cell8.06e-1718
CD14-positive, CD16-negative classical monocyte6.98e-1442
myeloid leukocyte1.08e-1376
classical monocyte1.93e-1245
T cell5.66e-1225
pro-T cell5.66e-1225
granulocyte monocyte progenitor cell3.34e-1171
CD4-positive, alpha-beta T cell3.78e-106
CD8-positive, alpha-beta T cell5.54e-1011
macrophage dendritic cell progenitor1.40e-0965
myeloid lineage restricted progenitor cell1.55e-0970
myeloid cell3.82e-09112
common myeloid progenitor3.82e-09112
lymphoid lineage restricted progenitor cell6.57e-0952
lymphocyte1.30e-0853
common lymphoid progenitor1.30e-0853
circulating cell2.31e-086
monopoietic cell3.08e-0863
monocyte3.08e-0863
monoblast3.08e-0863
promonocyte3.08e-0863
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.17e-16102
blood island1.17e-16102
hemolymphoid system8.81e-15112
bone marrow6.23e-0980
immune system7.87e-08115
bone element1.03e-0786
blood2.08e-0715
haemolymphatic fluid2.08e-0715
organism substance2.08e-0715


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.