Personal tools

Coexpression cluster:C1176: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C1176_acute_biphenotypic_Adipocyte_myelodysplastic_Preadipocyte_CD14_granulocyte |id=C1176 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C1176_acute_biphenotypic_Adipocyte_myelodysplastic_Preadipocyte_CD14_granulocyte
|full_id=C1176_acute_biphenotypic_Adipocyte_myelodysplastic_Preadipocyte_CD14_granulocyte
|id=C1176
|id=C1176
|ontology_enrichment_celltype=CL:0002057!5.67e-33!42;CL:0000860!5.11e-31!45;CL:0000763!8.36e-30!112;CL:0000049!8.36e-30!112;CL:0000766!8.68e-27!76;CL:0002194!3.67e-23!63;CL:0000576!3.67e-23!63;CL:0000040!3.67e-23!63;CL:0000559!3.67e-23!63;CL:0002009!6.53e-23!65;CL:0000557!1.15e-21!71;CL:0000037!1.72e-21!172;CL:0000566!1.72e-21!172;CL:0000839!4.81e-21!70;CL:0002032!2.15e-19!165;CL:0000837!2.15e-19!165;CL:0000988!1.09e-18!182;CL:0000738!1.82e-15!140;CL:0002087!3.76e-13!119;CL:0002031!8.74e-11!124;CL:0002393!8.07e-09!9;CL:0002397!8.07e-09!9;CL:0000094!7.06e-08!8;CL:0000134!7.32e-07!358
|ontology_enrichment_disease=DOID:1240!2.68e-07!39;DOID:8692!2.86e-07!31;DOID:2531!6.43e-07!51;DOID:0060083!6.43e-07!51
|ontology_enrichment_uberon=UBERON:0002371!3.42e-19!80;UBERON:0002390!1.05e-18!102;UBERON:0003061!1.05e-18!102;UBERON:0002193!1.44e-17!112;UBERON:0001474!1.35e-16!86;UBERON:0002405!8.70e-14!115;UBERON:0004765!6.01e-13!101;UBERON:0001434!6.01e-13!101;UBERON:0007023!1.31e-09!115;UBERON:0001049!2.20e-08!57;UBERON:0005068!2.20e-08!57;UBERON:0006241!2.20e-08!57;UBERON:0007135!2.20e-08!57
}}
}}

Revision as of 14:08, 21 May 2012


Full id: C1176_acute_biphenotypic_Adipocyte_myelodysplastic_Preadipocyte_CD14_granulocyte



Phase1 CAGE Peaks

Hg19::chr12:78430380..78430417,+p10@NAV3
Hg19::chr17:56367207..56367226,+p@chr17:56367207..56367226
+
Hg19::chr17:79795485..79795489,-p@chr17:79795485..79795489
-
Hg19::chr17:79795700..79795722,-p@chr17:79795700..79795722
-
Hg19::chr1:243893553..243893562,+p@chr1:243893553..243893562
+
Hg19::chr4:154649390..154649401,-p@chr4:154649390..154649401
-
Hg19::chr4:154649405..154649422,-p@chr4:154649405..154649422
-


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
CD14-positive, CD16-negative classical monocyte5.67e-3342
classical monocyte5.11e-3145
myeloid cell8.36e-30112
common myeloid progenitor8.36e-30112
myeloid leukocyte8.68e-2776
monopoietic cell3.67e-2363
monocyte3.67e-2363
monoblast3.67e-2363
promonocyte3.67e-2363
macrophage dendritic cell progenitor6.53e-2365
granulocyte monocyte progenitor cell1.15e-2171
hematopoietic stem cell1.72e-21172
angioblastic mesenchymal cell1.72e-21172
myeloid lineage restricted progenitor cell4.81e-2170
hematopoietic oligopotent progenitor cell2.15e-19165
hematopoietic multipotent progenitor cell2.15e-19165
hematopoietic cell1.09e-18182
leukocyte1.82e-15140
nongranular leukocyte3.76e-13119
hematopoietic lineage restricted progenitor cell8.74e-11124
intermediate monocyte8.07e-099
CD14-positive, CD16-positive monocyte8.07e-099
granulocyte7.06e-088
mesenchymal cell7.32e-07358
Uber Anatomy
Ontology termp-valuen
bone marrow3.42e-1980
hematopoietic system1.05e-18102
blood island1.05e-18102
hemolymphoid system1.44e-17112
bone element1.35e-1686
immune system8.70e-14115
skeletal element6.01e-13101
skeletal system6.01e-13101
adult organism1.31e-09115
neural tube2.20e-0857
neural rod2.20e-0857
future spinal cord2.20e-0857
neural keel2.20e-0857
Disease
Ontology termp-valuen
leukemia2.68e-0739
myeloid leukemia2.86e-0731
hematologic cancer6.43e-0751
immune system cancer6.43e-0751


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.