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Coexpression cluster:C1650: Difference between revisions

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|full_id=C1650_Monocytederived_CD14_Skeletal_Mast_melanoma_Melanocyte_nasal
|full_id=C1650_Monocytederived_CD14_Skeletal_Mast_melanoma_Melanocyte_nasal
|id=C1650
|id=C1650
|ontology_enrichment_celltype=CL:0000557!1.73e-26!71;CL:0002009!6.79e-25!65;CL:0000839!1.17e-24!70;CL:0002194!9.35e-24!63;CL:0000576!9.35e-24!63;CL:0000040!9.35e-24!63;CL:0000559!9.35e-24!63;CL:0000766!4.28e-22!76;CL:0002057!1.42e-21!42;CL:0000860!4.63e-19!45;CL:0000763!1.20e-13!112;CL:0000049!1.20e-13!112;CL:0002031!1.25e-07!124
|ontology_enrichment_celltype=CL:0000235!1.17e-43!6;CL:0000839!2.65e-39!66;CL:0000557!1.13e-38!67;CL:0000766!9.05e-36!72;CL:0002194!1.41e-35!59;CL:0000576!1.41e-35!59;CL:0000040!1.41e-35!59;CL:0000559!1.41e-35!59;CL:0002009!2.55e-34!61;CL:0000473!3.47e-31!48;CL:0000234!3.47e-31!48;CL:0000763!1.01e-22!108;CL:0000049!1.01e-22!108;CL:0002031!4.30e-20!120;CL:0000325!3.12e-18!87;CL:0000738!2.65e-17!136;CL:0002087!9.67e-17!115;CL:0002032!4.80e-14!161;CL:0000837!4.80e-14!161;CL:0000037!2.64e-13!168;CL:0000566!2.64e-13!168;CL:0000860!1.47e-12!42;CL:0002057!1.47e-12!42;CL:0000988!1.94e-12!177;CL:0002619!1.87e-10!3;CL:0002566!3.06e-08!1
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002371!5.51e-23!80;UBERON:0001474!1.18e-20!86;UBERON:0004765!9.36e-16!101;UBERON:0001434!9.36e-16!101;UBERON:0002405!1.86e-15!115;UBERON:0002390!2.94e-14!102;UBERON:0003061!2.94e-14!102;UBERON:0002193!7.53e-14!112;UBERON:0002204!4.51e-12!167;UBERON:0000062!7.71e-08!511
|ontology_enrichment_uberon=UBERON:0002371!1.02e-33!76;UBERON:0001474!5.17e-31!82;UBERON:0004765!5.86e-28!90;UBERON:0002405!6.03e-27!93;UBERON:0002390!2.14e-25!98;UBERON:0003061!2.14e-25!98;UBERON:0001434!8.08e-25!100;UBERON:0002193!1.01e-22!108;UBERON:0002204!5.54e-15!167;UBERON:0003081!1.20e-11!203;UBERON:0002171!8.78e-09!1;UBERON:0006518!8.78e-09!1;UBERON:0008949!8.78e-09!1;UBERON:0000101!8.78e-09!1;UBERON:0002167!8.78e-09!1;UBERON:0000926!7.51e-08!315;UBERON:0004120!7.51e-08!315;UBERON:0006603!7.51e-08!315
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}}
}}

Revision as of 11:32, 19 October 2012


Full id: C1650_Monocytederived_CD14_Skeletal_Mast_melanoma_Melanocyte_nasal



Phase1 CAGE Peaks

Hg19::chr11:92616200..92616202,+p4@FAT3
Hg19::chr12:111752856..111752859,-p@chr12:111752856..111752859
-
Hg19::chr19:2766953..2766958,+p@chr19:2766953..2766958
+
Hg19::chr6:170124005..170124009,+p@chr6:170124005..170124009
+
Hg19::chr7:150574212..150574225,-p@chr7:150574212..150574225
-


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
macrophage1.17e-436
myeloid lineage restricted progenitor cell2.65e-3966
granulocyte monocyte progenitor cell1.13e-3867
myeloid leukocyte9.05e-3672
monopoietic cell1.41e-3559
monocyte1.41e-3559
monoblast1.41e-3559
promonocyte1.41e-3559
macrophage dendritic cell progenitor2.55e-3461
defensive cell3.47e-3148
phagocyte3.47e-3148
myeloid cell1.01e-22108
common myeloid progenitor1.01e-22108
hematopoietic lineage restricted progenitor cell4.30e-20120
stuff accumulating cell3.12e-1887
leukocyte2.65e-17136
nongranular leukocyte9.67e-17115
hematopoietic oligopotent progenitor cell4.80e-14161
hematopoietic multipotent progenitor cell4.80e-14161
hematopoietic stem cell2.64e-13168
angioblastic mesenchymal cell2.64e-13168
classical monocyte1.47e-1242
CD14-positive, CD16-negative classical monocyte1.47e-1242
hematopoietic cell1.94e-12177
adult endothelial progenitor cell1.87e-103
dark melanocyte3.06e-081
Uber Anatomy
Ontology termp-valuen
bone marrow1.02e-3376
bone element5.17e-3182
skeletal element5.86e-2890
immune system6.03e-2793
hematopoietic system2.14e-2598
blood island2.14e-2598
skeletal system8.08e-25100
hemolymphoid system1.01e-22108
musculoskeletal system5.54e-15167
lateral plate mesoderm1.20e-11203
lower lobe of right lung8.78e-091
right lung lobe8.78e-091
lower lobe of lung8.78e-091
lobe of lung8.78e-091
right lung8.78e-091
mesoderm7.51e-08315
mesoderm-derived structure7.51e-08315
presumptive mesoderm7.51e-08315


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


No analysis results for this cluster

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.