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Coexpression cluster:C4135: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!3.54e-14!102;UBERON:0003061!3.54e-14!102;UBERON:0002371!1.49e-13!80;UBERON:0001474!1.56e-13!86;UBERON:0002193!1.55e-12!112;UBERON:0004765!1.88e-09!101;UBERON:0001434!1.88e-09!101;UBERON:0002405!2.03e-08!115
|ontology_enrichment_uberon=UBERON:0002390!3.54e-14!102;UBERON:0003061!3.54e-14!102;UBERON:0002371!1.49e-13!80;UBERON:0001474!1.56e-13!86;UBERON:0002193!1.55e-12!112;UBERON:0004765!1.88e-09!101;UBERON:0001434!1.88e-09!101;UBERON:0002405!2.03e-08!115
|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259625458345963!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326108738487779!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323052103220695!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295094132729292!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270077111719419!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173223337458314!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203430541796766!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247017008317628!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614907858179525!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390218759881209
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}}
}}

Revision as of 12:58, 5 September 2012


Full id: C4135_Mast_CD14_CD19_Eosinophils_CD4_CD8_Natural



Phase1 CAGE Peaks

Hg19::chr2:157189816..157189856,+p@chr2:157189816..157189856
+
Hg19::chr8:102218069..102218077,+p@chr8:102218069..102218077
+
Hg19::chr8:102218099..102218114,+p@chr8:102218099..102218114
+


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
leukocyte1.46e-33140
hematopoietic stem cell5.91e-33172
angioblastic mesenchymal cell5.91e-33172
hematopoietic cell6.36e-31182
hematopoietic oligopotent progenitor cell2.32e-29165
hematopoietic multipotent progenitor cell2.32e-29165
CD14-positive, CD16-negative classical monocyte2.93e-2442
nongranular leukocyte3.68e-24119
hematopoietic lineage restricted progenitor cell7.38e-24124
classical monocyte1.83e-2345
myeloid cell1.17e-19112
common myeloid progenitor1.17e-19112
myeloid leukocyte1.20e-1976
granulocyte monocyte progenitor cell6.78e-1771
macrophage dendritic cell progenitor5.25e-1565
myeloid lineage restricted progenitor cell3.25e-1470
monopoietic cell5.23e-1463
monocyte5.23e-1463
monoblast5.23e-1463
promonocyte5.23e-1463
lymphocyte4.23e-0953
common lymphoid progenitor4.23e-0953
lymphoid lineage restricted progenitor cell5.77e-0952
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.54e-14102
blood island3.54e-14102
bone marrow1.49e-1380
bone element1.56e-1386
hemolymphoid system1.55e-12112
skeletal element1.88e-09101
skeletal system1.88e-09101
immune system2.03e-08115


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
ATF3#467214.97544968400580.005768294540793880.0259625458345963
E2F1#186934.907389214879320.008460985347239390.0326108738487779
E2F6#187635.017155731697390.00791769806886330.0323052103220695
MYC#460935.22228187160940.007020843755740150.0295094132729292
NFKB1#479035.488063424193840.006049381815655430.0270077111719419
PAX5#507936.669565531177830.003370290999677260.0173223337458314
SMARCB1#6598318.25271578115740.000164397760679890.00203430541796766
SP1#666735.69838137814090.005403962701712170.0247017008317628
TCF7L2#6934310.77017656313730.0008003181298398380.00614907858179525
TFAP2A#7020211.01242291536330.01054990655215560.0390218759881209



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.