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Coexpression cluster:C4471: Difference between revisions

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|full_id=C4471_CD14_B_b_xeroderma_CD4_Preadipocyte_testicular
|full_id=C4471_CD14_B_b_xeroderma_CD4_Preadipocyte_testicular
|id=C4471
|id=C4471
|ontology_enrichment_celltype=CL:0000738!7.07e-41!140;CL:0002031!1.15e-36!124;CL:0002087!2.01e-35!119;CL:0002032!1.01e-30!165;CL:0000837!1.01e-30!165;CL:0000037!7.24e-30!172;CL:0000566!7.24e-30!172;CL:0000988!2.09e-28!182;CL:0002057!5.91e-23!42;CL:0000860!6.52e-21!45;CL:0000542!2.06e-20!53;CL:0000051!2.06e-20!53;CL:0000838!2.44e-19!52;CL:0000766!2.22e-18!76;CL:0000557!1.83e-17!71;CL:0000839!2.14e-16!70;CL:0002009!1.11e-15!65;CL:0002194!5.53e-15!63;CL:0000576!5.53e-15!63;CL:0000040!5.53e-15!63;CL:0000559!5.53e-15!63;CL:0000763!2.97e-12!112;CL:0000049!2.97e-12!112;CL:0000084!1.23e-09!25;CL:0000827!1.23e-09!25;CL:0000791!1.59e-08!18;CL:0000789!1.59e-08!18;CL:0002420!1.59e-08!18;CL:0002419!1.59e-08!18;CL:0000790!1.59e-08!18;CL:0000945!7.36e-08!24;CL:0000826!7.36e-08!24;CL:0000134!3.37e-07!358;CL:0002320!8.97e-07!365
|ontology_enrichment_celltype=CL:0000860!1.87e-39!42;CL:0002057!1.87e-39!42;CL:0000473!3.89e-34!48;CL:0000234!3.89e-34!48;CL:0002009!3.67e-29!61;CL:0002031!6.71e-29!120;CL:0002087!1.17e-27!115;CL:0000738!2.27e-27!136;CL:0002194!1.09e-26!59;CL:0000576!1.09e-26!59;CL:0000040!1.09e-26!59;CL:0000559!1.09e-26!59;CL:0000557!2.69e-26!67;CL:0000766!2.97e-24!72;CL:0000839!1.42e-23!66;CL:0002032!1.86e-22!161;CL:0000837!1.86e-22!161;CL:0000037!2.43e-21!168;CL:0000566!2.43e-21!168;CL:0000988!4.92e-20!177;CL:0000325!1.97e-17!87;CL:0000763!3.79e-17!108;CL:0000049!3.79e-17!108;CL:0000945!1.67e-13!24;CL:0000826!1.67e-13!24;CL:0000946!5.82e-08!1;CL:0000786!5.82e-08!1;CL:0000980!5.82e-08!1;CL:0000134!9.78e-08!354;CL:0002320!1.70e-07!361
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:630!1.88e-08!1;DOID:0050177!1.88e-08!1;DOID:0050427!1.88e-08!1
|ontology_enrichment_uberon=UBERON:0002390!3.44e-16!102;UBERON:0003061!3.44e-16!102;UBERON:0002193!9.25e-15!112;UBERON:0002371!1.56e-14!80;UBERON:0002405!3.60e-13!115;UBERON:0001474!6.23e-13!86;UBERON:0004765!1.78e-12!101;UBERON:0001434!1.78e-12!101
|ontology_enrichment_uberon=UBERON:0002405!6.55e-23!93;UBERON:0002371!7.81e-23!76;UBERON:0002390!1.44e-21!98;UBERON:0003061!1.44e-21!98;UBERON:0001474!6.08e-21!82;UBERON:0002193!3.00e-19!108;UBERON:0004765!8.28e-19!90;UBERON:0001434!1.29e-16!100;UBERON:0002204!1.16e-08!167;UBERON:0003081!1.47e-08!203;UBERON:0002384!3.63e-07!371
|tf_chipseq_enrich=BATF#10538;2:16.2385345282024:0.00491746240780997:0.0230044728514789!BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.01839500310577!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00918388853723452!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195396026197541!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270551296439379
|tf_chipseq_enrich=BATF#10538;2:16.2385345282024:0.00491746240780997:0.0230044728514789!BCL11A#53335;2:18.9129700690714:0.00363940624837968:0.01839500310577!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00918388853723452!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195396026197541!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270551296439379
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}}
}}

Revision as of 15:58, 19 October 2012


Full id: C4471_CD14_B_b_xeroderma_CD4_Preadipocyte_testicular



Phase1 CAGE Peaks

Hg19::chr5:142415993..142416004,+p@chr5:142415993..142416004
+
Hg19::chr5:158885630..158885652,+p@chr5:158885630..158885652
+
Hg19::chr8:101455606..101455618,+p@chr8:101455606..101455618
+


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
classical monocyte1.87e-3942
CD14-positive, CD16-negative classical monocyte1.87e-3942
defensive cell3.89e-3448
phagocyte3.89e-3448
macrophage dendritic cell progenitor3.67e-2961
hematopoietic lineage restricted progenitor cell6.71e-29120
nongranular leukocyte1.17e-27115
leukocyte2.27e-27136
monopoietic cell1.09e-2659
monocyte1.09e-2659
monoblast1.09e-2659
promonocyte1.09e-2659
granulocyte monocyte progenitor cell2.69e-2667
myeloid leukocyte2.97e-2472
myeloid lineage restricted progenitor cell1.42e-2366
hematopoietic oligopotent progenitor cell1.86e-22161
hematopoietic multipotent progenitor cell1.86e-22161
hematopoietic stem cell2.43e-21168
angioblastic mesenchymal cell2.43e-21168
hematopoietic cell4.92e-20177
stuff accumulating cell1.97e-1787
myeloid cell3.79e-17108
common myeloid progenitor3.79e-17108
lymphocyte of B lineage1.67e-1324
pro-B cell1.67e-1324
antibody secreting cell5.82e-081
plasma cell5.82e-081
plasmablast5.82e-081
mesenchymal cell9.78e-08354
connective tissue cell1.70e-07361
Uber Anatomy
Ontology termp-valuen
immune system6.55e-2393
bone marrow7.81e-2376
hematopoietic system1.44e-2198
blood island1.44e-2198
bone element6.08e-2182
hemolymphoid system3.00e-19108
skeletal element8.28e-1990
skeletal system1.29e-16100
musculoskeletal system1.16e-08167
lateral plate mesoderm1.47e-08203
connective tissue3.63e-07371
Disease
Ontology termp-valuen
genetic disease1.88e-081
monogenic disease1.88e-081
xeroderma pigmentosum1.88e-081


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#10538216.23853452820240.004917462407809970.0230044728514789
BCL11A#53335218.91297006907140.003639406248379680.01839500310577
EBF1#187938.9064668465690.00141523283560980.00918388853723452
MEF2A#4205318.74323090964410.0001518243905622470.00195396026197541
NFKB1#479035.488063424193840.006049381815655430.0270551296439379



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.