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Coexpression cluster:C3506: Difference between revisions

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|full_id=C3506_Melanocyte_CD14_melanoma_Mesenchymal_Monocytederived_Fibroblast_tridermal
|full_id=C3506_Melanocyte_CD14_melanoma_Mesenchymal_Monocytederived_Fibroblast_tridermal
|id=C3506
|id=C3506
|ontology_enrichment_celltype=CL:0002009!1.05e-34!65;CL:0002194!1.18e-34!63;CL:0000576!1.18e-34!63;CL:0000040!1.18e-34!63;CL:0000559!1.18e-34!63;CL:0000557!3.89e-34!71;CL:0000766!1.79e-33!76;CL:0000839!2.98e-33!70;CL:0002057!4.61e-33!42;CL:0000860!8.54e-30!45;CL:0000763!7.98e-28!112;CL:0000049!7.98e-28!112;CL:0002031!1.10e-23!124;CL:0002032!1.65e-22!165;CL:0000837!1.65e-22!165;CL:0000738!6.75e-22!140;CL:0002087!7.61e-22!119;CL:0000037!2.81e-21!172;CL:0000566!2.81e-21!172;CL:0000988!3.03e-19!182;CL:0000219!3.28e-09!390;CL:0000134!5.27e-08!358;CL:0000148!2.05e-07!10;CL:0000541!2.05e-07!10;CL:0002320!2.44e-07!365
|ontology_enrichment_celltype=CL:0000473!2.09e-59!48;CL:0000234!2.09e-59!48;CL:0000860!4.60e-55!42;CL:0002057!4.60e-55!42;CL:0000325!1.09e-51!87;CL:0002009!1.47e-47!61;CL:0002194!5.05e-46!59;CL:0000576!5.05e-46!59;CL:0000040!5.05e-46!59;CL:0000559!5.05e-46!59;CL:0000557!1.12e-45!67;CL:0000839!2.30e-43!66;CL:0000766!3.61e-39!72;CL:0000763!1.81e-29!108;CL:0000049!1.81e-29!108;CL:0002031!5.84e-24!120;CL:0002087!6.73e-22!115;CL:0000738!3.09e-20!136;CL:0000148!4.58e-19!10;CL:0000541!4.58e-19!10;CL:0002032!1.70e-18!161;CL:0000837!1.70e-18!161;CL:0000037!2.17e-17!168;CL:0000566!2.17e-17!168;CL:0000147!5.78e-17!14;CL:0000988!4.27e-16!177;CL:0002567!6.69e-13!3;CL:0000219!2.38e-10!386;CL:0000710!5.65e-09!20;CL:0000134!7.04e-07!354
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002371!2.94e-29!80;UBERON:0001474!7.90e-28!86;UBERON:0002405!8.27e-25!115;UBERON:0004765!1.23e-20!101;UBERON:0001434!1.23e-20!101;UBERON:0002390!3.83e-20!102;UBERON:0003061!3.83e-20!102;UBERON:0002193!3.52e-18!112;UBERON:0002204!2.58e-08!167;UBERON:0002384!8.99e-07!375
|ontology_enrichment_uberon=UBERON:0002371!2.04e-39!76;UBERON:0001474!5.36e-36!82;UBERON:0002405!4.85e-33!93;UBERON:0004765!3.84e-32!90;UBERON:0002390!6.51e-29!98;UBERON:0003061!6.51e-29!98;UBERON:0001434!3.48e-28!100;UBERON:0002193!2.17e-27!108;UBERON:0002204!4.86e-15!167;UBERON:0003081!5.86e-12!203;UBERON:0000926!8.45e-07!315;UBERON:0004120!8.45e-07!315;UBERON:0006603!8.45e-07!315
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460327464191481
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460327464191481
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}}
}}

Revision as of 15:10, 19 October 2012


Full id: C3506_Melanocyte_CD14_melanoma_Mesenchymal_Monocytederived_Fibroblast_tridermal



Phase1 CAGE Peaks

Hg19::chr15:68574500..68574509,+p@chr15:68574500..68574509
+
Hg19::chr16:1524955..1524963,-p1@CU680386
Hg19::chr18:74839891..74839921,-p@chr18:74839891..74839921
-


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
defensive cell2.09e-5948
phagocyte2.09e-5948
classical monocyte4.60e-5542
CD14-positive, CD16-negative classical monocyte4.60e-5542
stuff accumulating cell1.09e-5187
macrophage dendritic cell progenitor1.47e-4761
monopoietic cell5.05e-4659
monocyte5.05e-4659
monoblast5.05e-4659
promonocyte5.05e-4659
granulocyte monocyte progenitor cell1.12e-4567
myeloid lineage restricted progenitor cell2.30e-4366
myeloid leukocyte3.61e-3972
myeloid cell1.81e-29108
common myeloid progenitor1.81e-29108
hematopoietic lineage restricted progenitor cell5.84e-24120
nongranular leukocyte6.73e-22115
leukocyte3.09e-20136
melanocyte4.58e-1910
melanoblast4.58e-1910
hematopoietic oligopotent progenitor cell1.70e-18161
hematopoietic multipotent progenitor cell1.70e-18161
hematopoietic stem cell2.17e-17168
angioblastic mesenchymal cell2.17e-17168
pigment cell5.78e-1714
hematopoietic cell4.27e-16177
light melanocyte6.69e-133
motile cell2.38e-10386
neurecto-epithelial cell5.65e-0920
mesenchymal cell7.04e-07354
Uber Anatomy
Ontology termp-valuen
bone marrow2.04e-3976
bone element5.36e-3682
immune system4.85e-3393
skeletal element3.84e-3290
hematopoietic system6.51e-2998
blood island6.51e-2998
skeletal system3.48e-28100
hemolymphoid system2.17e-27108
musculoskeletal system4.86e-15167
lateral plate mesoderm5.86e-12203
mesoderm8.45e-07315
mesoderm-derived structure8.45e-07315
presumptive mesoderm8.45e-07315


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
NR3C1#290829.982015554115360.01278474365547170.0460327464191481



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.