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Coexpression cluster:C4692: Difference between revisions

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|full_id=C4692_anaplastic_cord_Dendritic_hairy_chronic_CD14_acute
|full_id=C4692_anaplastic_cord_Dendritic_hairy_chronic_CD14_acute
|id=C4692
|id=C4692
|ontology_enrichment_celltype=CL:0000763!1.21e-47!112;CL:0000049!1.21e-47!112;CL:0000988!1.60e-44!182;CL:0000557!2.14e-40!71;CL:0002032!4.73e-40!165;CL:0000837!4.73e-40!165;CL:0000839!1.37e-39!70;CL:0000037!3.12e-39!172;CL:0000566!3.12e-39!172;CL:0002194!3.13e-39!63;CL:0000576!3.13e-39!63;CL:0000040!3.13e-39!63;CL:0000559!3.13e-39!63;CL:0002009!4.03e-39!65;CL:0000766!7.66e-38!76;CL:0002057!2.92e-35!42;CL:0000860!6.98e-32!45;CL:0002031!3.63e-29!124;CL:0000738!1.51e-28!140;CL:0002087!7.05e-28!119;CL:0002320!3.16e-11!365;CL:0000134!3.73e-11!358;CL:0000219!4.61e-09!390;CL:0000048!1.78e-08!430;CL:0000723!5.98e-08!436;CL:0000034!6.43e-08!444
|ontology_enrichment_celltype=CL:0000557!9.75e-42!67;CL:0002009!1.20e-41!61;CL:0002194!8.90e-41!59;CL:0000576!8.90e-41!59;CL:0000040!8.90e-41!59;CL:0000559!8.90e-41!59;CL:0000839!4.54e-40!66;CL:0000763!1.68e-39!108;CL:0000049!1.68e-39!108;CL:0000473!1.68e-37!48;CL:0000234!1.68e-37!48;CL:0000766!6.69e-36!72;CL:0000988!5.93e-34!177;CL:0002032!1.50e-33!161;CL:0000837!1.50e-33!161;CL:0000860!8.56e-32!42;CL:0002057!8.56e-32!42;CL:0000037!1.51e-31!168;CL:0000566!1.51e-31!168;CL:0002031!1.22e-30!120;CL:0002087!1.14e-27!115;CL:0000738!1.34e-25!136;CL:0000325!6.43e-17!87;CL:0000134!7.53e-09!354;CL:0002320!2.02e-08!361;CL:0000840!1.75e-07!5;CL:0001029!1.75e-07!5;CL:0000219!2.05e-07!386;CL:0000235!4.23e-07!6;CL:0000048!5.47e-07!427
|ontology_enrichment_disease=DOID:1240!7.98e-15!39;DOID:8692!1.83e-13!31;DOID:2531!3.90e-13!51;DOID:0060083!3.90e-13!51
|ontology_enrichment_disease=DOID:1240!3.84e-09!39;DOID:8692!7.19e-09!31;DOID:2531!2.03e-07!51;DOID:0060083!2.03e-07!51
|ontology_enrichment_uberon=UBERON:0002371!5.73e-35!80;UBERON:0002193!7.66e-33!112;UBERON:0001474!1.89e-32!86;UBERON:0002390!1.23e-31!102;UBERON:0003061!1.23e-31!102;UBERON:0002405!2.19e-27!115;UBERON:0004765!1.94e-26!101;UBERON:0001434!1.94e-26!101;UBERON:0003081!5.58e-14!216;UBERON:0002204!1.83e-13!167;UBERON:0002384!5.85e-11!375
|ontology_enrichment_uberon=UBERON:0002405!2.33e-36!93;UBERON:0002193!1.33e-35!108;UBERON:0002371!1.38e-35!76;UBERON:0002390!1.76e-34!98;UBERON:0003061!1.76e-34!98;UBERON:0001474!3.12e-32!82;UBERON:0004765!1.86e-28!90;UBERON:0001434!1.36e-24!100;UBERON:0003081!3.15e-13!203;UBERON:0002204!1.21e-11!167;UBERON:0002384!2.18e-08!371
|tf_chipseq_enrich=GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154808957593432!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393572060283661!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376476388901085
|tf_chipseq_enrich=GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154808957593432!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393572060283661!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376476388901085
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}}
}}

Revision as of 16:09, 19 October 2012


Full id: C4692_anaplastic_cord_Dendritic_hairy_chronic_CD14_acute



Phase1 CAGE Peaks

Hg19::chr7:643123..643163,+p@chr7:643123..643163
+
Hg19::chr7:643166..643188,+p@chr7:643166..643188
+
Hg19::chr7:643196..643205,+p@chr7:643196..643205
+


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
granulocyte monocyte progenitor cell9.75e-4267
macrophage dendritic cell progenitor1.20e-4161
monopoietic cell8.90e-4159
monocyte8.90e-4159
monoblast8.90e-4159
promonocyte8.90e-4159
myeloid lineage restricted progenitor cell4.54e-4066
myeloid cell1.68e-39108
common myeloid progenitor1.68e-39108
defensive cell1.68e-3748
phagocyte1.68e-3748
myeloid leukocyte6.69e-3672
hematopoietic cell5.93e-34177
hematopoietic oligopotent progenitor cell1.50e-33161
hematopoietic multipotent progenitor cell1.50e-33161
classical monocyte8.56e-3242
CD14-positive, CD16-negative classical monocyte8.56e-3242
hematopoietic stem cell1.51e-31168
angioblastic mesenchymal cell1.51e-31168
hematopoietic lineage restricted progenitor cell1.22e-30120
nongranular leukocyte1.14e-27115
leukocyte1.34e-25136
stuff accumulating cell6.43e-1787
mesenchymal cell7.53e-09354
connective tissue cell2.02e-08361
immature conventional dendritic cell1.75e-075
common dendritic progenitor1.75e-075
motile cell2.05e-07386
macrophage4.23e-076
multi fate stem cell5.47e-07427
Uber Anatomy
Ontology termp-valuen
immune system2.33e-3693
hemolymphoid system1.33e-35108
bone marrow1.38e-3576
hematopoietic system1.76e-3498
blood island1.76e-3498
bone element3.12e-3282
skeletal element1.86e-2890
skeletal system1.36e-24100
lateral plate mesoderm3.15e-13203
musculoskeletal system1.21e-11167
connective tissue2.18e-08371
Disease
Ontology termp-valuen
leukemia3.84e-0939
myeloid leukemia7.19e-0931
hematologic cancer2.03e-0751
immune system cancer2.03e-0751


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
GABPB1#255337.067683836182170.002832212825417420.0154808957593432
HDAC2#3066313.41562023662630.0004140761399857210.00393572060283661
SRF#6722313.79717826216780.0003806615025800190.00376476388901085



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.