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Coexpression cluster:C3365: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!6.37e-33!102;UBERON:0003061!6.37e-33!102;UBERON:0002193!4.47e-32!112;UBERON:0002371!1.98e-24!80;UBERON:0007023!2.42e-24!115;UBERON:0002405!9.31e-23!115;UBERON:0001474!7.54e-22!86;UBERON:0004765!2.35e-16!101;UBERON:0001434!2.35e-16!101;UBERON:0001049!5.66e-10!57;UBERON:0005068!5.66e-10!57;UBERON:0006241!5.66e-10!57;UBERON:0007135!5.66e-10!57;UBERON:0003080!6.62e-09!42;UBERON:0002780!1.34e-08!41;UBERON:0001890!1.34e-08!41;UBERON:0006240!1.34e-08!41;UBERON:0002020!1.66e-07!34;UBERON:0003528!1.66e-07!34;UBERON:0000178!2.04e-07!15;UBERON:0000179!2.04e-07!15;UBERON:0000463!2.04e-07!15;UBERON:0001893!2.05e-07!34;UBERON:0002384!2.26e-07!375;UBERON:0002791!3.05e-07!33;UBERON:0002616!3.17e-07!59;UBERON:0001869!5.50e-07!32;UBERON:0002619!7.76e-07!22
|ontology_enrichment_uberon=UBERON:0002390!6.37e-33!102;UBERON:0003061!6.37e-33!102;UBERON:0002193!4.47e-32!112;UBERON:0002371!1.98e-24!80;UBERON:0007023!2.42e-24!115;UBERON:0002405!9.31e-23!115;UBERON:0001474!7.54e-22!86;UBERON:0004765!2.35e-16!101;UBERON:0001434!2.35e-16!101;UBERON:0001049!5.66e-10!57;UBERON:0005068!5.66e-10!57;UBERON:0006241!5.66e-10!57;UBERON:0007135!5.66e-10!57;UBERON:0003080!6.62e-09!42;UBERON:0002780!1.34e-08!41;UBERON:0001890!1.34e-08!41;UBERON:0006240!1.34e-08!41;UBERON:0002020!1.66e-07!34;UBERON:0003528!1.66e-07!34;UBERON:0000178!2.04e-07!15;UBERON:0000179!2.04e-07!15;UBERON:0000463!2.04e-07!15;UBERON:0001893!2.05e-07!34;UBERON:0002384!2.26e-07!375;UBERON:0002791!3.05e-07!33;UBERON:0002616!3.17e-07!59;UBERON:0001869!5.50e-07!32;UBERON:0002619!7.76e-07!22
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319624525956387!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046079812969112!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268996205324323!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172544030252595!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00164973081758805!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457205365910922!USF1#7391;3:6.36149927720796:0.0038840405729056:0.018980222412207
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}}
}}

Revision as of 13:37, 5 September 2012


Full id: C3365_Dendritic_immature_chronic_CD19_migratory_CD14_blood



Phase1 CAGE Peaks

Hg19::chr13:33002253..33002273,-p1@N4BP2L1
Hg19::chr1:153919349..153919375,-p7@DENND4B
Hg19::chr6:292982..293002,+p@chr6:292982..293002
+


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
hematopoietic stem cell1.22e-56172
angioblastic mesenchymal cell1.22e-56172
leukocyte1.65e-55140
hematopoietic cell8.44e-55182
hematopoietic oligopotent progenitor cell1.61e-52165
hematopoietic multipotent progenitor cell1.61e-52165
hematopoietic lineage restricted progenitor cell7.23e-45124
nongranular leukocyte1.28e-43119
myeloid cell1.50e-32112
common myeloid progenitor1.50e-32112
myeloid leukocyte2.23e-2976
granulocyte monocyte progenitor cell4.25e-2771
CD14-positive, CD16-negative classical monocyte7.83e-2642
myeloid lineage restricted progenitor cell4.83e-2570
macrophage dendritic cell progenitor6.64e-2565
monopoietic cell1.46e-2363
monocyte1.46e-2363
monoblast1.46e-2363
promonocyte1.46e-2363
classical monocyte1.17e-2145
lymphocyte2.34e-1753
common lymphoid progenitor2.34e-1753
lymphoid lineage restricted progenitor cell2.49e-1752
lymphocyte of B lineage1.68e-1024
pro-B cell1.68e-1024
mesenchymal cell1.55e-08358
dendritic cell2.58e-0810
connective tissue cell3.52e-08365
B cell1.41e-0714
intermediate monocyte4.70e-079
CD14-positive, CD16-positive monocyte4.70e-079
conventional dendritic cell5.94e-078
T cell7.80e-0725
pro-T cell7.80e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.37e-33102
blood island6.37e-33102
hemolymphoid system4.47e-32112
bone marrow1.98e-2480
adult organism2.42e-24115
immune system9.31e-23115
bone element7.54e-2286
skeletal element2.35e-16101
skeletal system2.35e-16101
neural tube5.66e-1057
neural rod5.66e-1057
future spinal cord5.66e-1057
neural keel5.66e-1057
anterior neural tube6.62e-0942
regional part of forebrain1.34e-0841
forebrain1.34e-0841
future forebrain1.34e-0841
gray matter1.66e-0734
brain grey matter1.66e-0734
blood2.04e-0715
haemolymphatic fluid2.04e-0715
organism substance2.04e-0715
telencephalon2.05e-0734
connective tissue2.26e-07375
regional part of telencephalon3.05e-0733
regional part of brain3.17e-0759
cerebral hemisphere5.50e-0732
regional part of cerebral cortex7.76e-0722


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
EGR1#195834.988179094810140.008056488137383440.0319624525956387
ELF1#199734.258097958807540.01295179875054610.046079812969112
NFKB1#479035.488063424193840.006049381815655430.0268996205324323
PAX5#507936.669565531177830.003370290999677260.0172544030252595
RXRA#6256320.07461713913330.0001235730348432220.00164973081758805
SMC3#9126210.02995522995520.0126656379767470.0457205365910922
USF1#739136.361499277207960.00388404057290560.018980222412207



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.