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Coexpression cluster:C3721: Difference between revisions

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|full_id=C3721_Macrophage_fibrous_anaplastic_Renal_serous_Monocytederived_small
|full_id=C3721_Macrophage_fibrous_anaplastic_Renal_serous_Monocytederived_small
|id=C3721
|id=C3721
|ontology_enrichment_celltype=CL:0002371!3.78e-18!591;CL:0000048!9.32e-16!430;CL:0000144!1.89e-15!625;CL:0000723!4.20e-15!436;CL:0000548!3.65e-14!679;CL:0000004!3.65e-14!679;CL:0000255!3.65e-14!679;CL:0000034!4.33e-14!444;CL:0000012!1.02e-13!682;CL:0000055!1.76e-13!180;CL:0002194!1.40e-10!63;CL:0000576!1.40e-10!63;CL:0000040!1.40e-10!63;CL:0000559!1.40e-10!63;CL:0002009!1.87e-10!65;CL:0002320!3.09e-10!365;CL:1000449!5.40e-10!16;CL:1000497!4.11e-09!18;CL:0002518!4.11e-09!18;CL:0000219!4.29e-09!390;CL:1000507!6.04e-09!12;CL:1000494!6.04e-09!12;CL:0000134!1.58e-08!358;CL:0000183!2.08e-08!59;CL:0000557!2.10e-08!71;CL:0000003!2.60e-08!722;CL:0000839!3.63e-08!70;CL:0000680!3.64e-08!57;CL:0000056!3.64e-08!57;CL:0000355!3.64e-08!57;CL:0002681!1.49e-07!13;CL:0002584!1.49e-07!13;CL:0000057!3.52e-07!75;CL:0000187!4.94e-07!54;CL:0000766!5.45e-07!76;CL:0000359!5.97e-07!32
|ontology_enrichment_celltype=CL:1000507!5.79e-14!10;CL:1000494!5.79e-14!10;CL:0002194!6.88e-13!59;CL:0000576!6.88e-13!59;CL:0000040!6.88e-13!59;CL:0000559!6.88e-13!59;CL:1000449!2.98e-12!15;CL:0002009!3.79e-12!61;CL:0002371!4.09e-12!588;CL:0000048!1.11e-10!427;CL:0000839!1.65e-10!66;CL:0000723!1.73e-10!433;CL:1000497!2.45e-10!17;CL:0002518!2.45e-10!17;CL:0000557!3.25e-10!67;CL:0000548!6.75e-10!679;CL:0000255!6.75e-10!679;CL:0000034!9.66e-10!441;CL:0000235!2.69e-09!6;CL:0000766!7.07e-09!72;CL:0002681!8.30e-09!12;CL:0002584!8.30e-09!12;CL:0000473!1.78e-08!48;CL:0000234!1.78e-08!48;CL:0002320!4.34e-08!361;CL:0000134!3.89e-07!354;CL:0000219!8.95e-07!386
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002204!1.56e-17!167;UBERON:0003081!6.25e-11!216;UBERON:0002371!1.03e-10!80;UBERON:0002384!3.63e-10!375;UBERON:0004211!5.40e-10!16;UBERON:0001285!5.40e-10!16;UBERON:0007684!5.40e-10!16;UBERON:0003220!5.40e-10!16;UBERON:0004208!5.40e-10!16;UBERON:0004765!1.39e-09!101;UBERON:0001434!1.39e-09!101;UBERON:0000914!1.62e-09!83;UBERON:0002329!1.62e-09!83;UBERON:0003077!1.62e-09!83;UBERON:0003059!1.62e-09!83;UBERON:0007282!1.62e-09!83;UBERON:0009618!1.62e-09!83;UBERON:0007285!1.62e-09!83;UBERON:0001474!1.70e-09!86;UBERON:0006555!4.73e-09!17;UBERON:0005103!4.73e-09!17;UBERON:0000083!4.73e-09!17;UBERON:0009201!4.73e-09!17;UBERON:0004819!4.73e-09!17;UBERON:0006553!4.73e-09!17;UBERON:0003074!4.73e-09!17;UBERON:0003060!4.73e-09!17;UBERON:0004290!5.99e-09!70;UBERON:0009773!6.04e-09!12;UBERON:0001231!6.04e-09!12;UBERON:0004810!6.04e-09!12;UBERON:0005256!7.94e-09!143;UBERON:0000486!2.86e-08!82;UBERON:0000080!3.18e-08!18;UBERON:0002120!3.18e-08!18;UBERON:0004875!3.18e-08!18;UBERON:0005721!3.18e-08!18;UBERON:0005754!3.18e-08!18;UBERON:0007297!3.18e-08!18;UBERON:0002405!4.23e-08!115;UBERON:0003887!5.23e-08!21;UBERON:0000353!1.11e-07!17;UBERON:0001225!1.49e-07!13;UBERON:0008987!1.49e-07!13;UBERON:0001134!2.76e-07!61;UBERON:0002036!2.76e-07!61;UBERON:0003082!2.76e-07!61;UBERON:0002385!3.11e-07!63;UBERON:0001015!3.11e-07!63;UBERON:0000383!3.11e-07!63;UBERON:0002193!6.80e-07!112;UBERON:0004876!7.66e-07!20
|ontology_enrichment_uberon=UBERON:0002204!1.73e-14!167;UBERON:0004810!5.79e-14!10;UBERON:0004211!2.98e-12!15;UBERON:0009773!2.98e-12!15;UBERON:0001231!2.98e-12!15;UBERON:0001285!2.98e-12!15;UBERON:0007684!2.98e-12!15;UBERON:0004208!2.98e-12!15;UBERON:0001434!1.50e-11!100;UBERON:0006555!3.12e-11!16;UBERON:0004819!3.12e-11!16;UBERON:0002371!8.08e-11!76;UBERON:0004765!2.37e-10!90;UBERON:0001474!4.52e-10!82;UBERON:0000926!2.64e-09!315;UBERON:0004120!2.64e-09!315;UBERON:0006603!2.64e-09!315;UBERON:0002405!3.18e-09!93;UBERON:0001225!8.30e-09!12;UBERON:0008987!8.30e-09!12;UBERON:0000353!4.02e-08!15;UBERON:0002384!1.43e-07!371
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00897180018226028
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00897180018226028
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}}
}}

Revision as of 15:20, 19 October 2012


Full id: C3721_Macrophage_fibrous_anaplastic_Renal_serous_Monocytederived_small



Phase1 CAGE Peaks

Hg19::chr18:43405525..43405545,+p3@SIGLEC15
Hg19::chr18:43405633..43405645,+p4@SIGLEC15
Hg19::chr18:43405655..43405696,+p1@SIGLEC15


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
kidney tubule cell5.79e-1410
nephron tubule epithelial cell5.79e-1410
monopoietic cell6.88e-1359
monocyte6.88e-1359
monoblast6.88e-1359
promonocyte6.88e-1359
epithelial cell of nephron2.98e-1215
macrophage dendritic cell progenitor3.79e-1261
somatic cell4.09e-12588
multi fate stem cell1.11e-10427
myeloid lineage restricted progenitor cell1.65e-1066
somatic stem cell1.73e-10433
kidney cell2.45e-1017
kidney epithelial cell2.45e-1017
granulocyte monocyte progenitor cell3.25e-1067
animal cell6.75e-10679
eukaryotic cell6.75e-10679
stem cell9.66e-10441
macrophage2.69e-096
myeloid leukocyte7.07e-0972
kidney cortical cell8.30e-0912
renal cortical epithelial cell8.30e-0912
defensive cell1.78e-0848
phagocyte1.78e-0848
connective tissue cell4.34e-08361
mesenchymal cell3.89e-07354
motile cell8.95e-07386
Uber Anatomy
Ontology termp-valuen
musculoskeletal system1.73e-14167
nephron tubule epithelium5.79e-1410
nephron epithelium2.98e-1215
renal tubule2.98e-1215
nephron tubule2.98e-1215
nephron2.98e-1215
uriniferous tubule2.98e-1215
nephrogenic mesenchyme2.98e-1215
skeletal system1.50e-11100
excretory tube3.12e-1116
kidney epithelium3.12e-1116
bone marrow8.08e-1176
skeletal element2.37e-1090
bone element4.52e-1082
mesoderm2.64e-09315
mesoderm-derived structure2.64e-09315
presumptive mesoderm2.64e-09315
immune system3.18e-0993
cortex of kidney8.30e-0912
renal parenchyma8.30e-0912
parenchyma4.02e-0815
connective tissue1.43e-07371


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
FOS#235338.99795530889440.001372499272417130.00897180018226028



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.

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