Personal tools

Coexpression cluster:C3491: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C3491_migratory_CD4_splenic_immature_xeroderma_b_lymphangiectasia |id=C3491 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C3491_migratory_CD4_splenic_immature_xeroderma_b_lymphangiectasia
|full_id=C3491_migratory_CD4_splenic_immature_xeroderma_b_lymphangiectasia
|id=C3491
|id=C3491
|ontology_enrichment_celltype=CL:0000738!4.70e-55!140;CL:0002087!3.51e-51!119;CL:0000037!6.05e-51!172;CL:0000566!6.05e-51!172;CL:0000988!8.53e-50!182;CL:0002032!2.65e-48!165;CL:0000837!2.65e-48!165;CL:0002031!1.22e-47!124;CL:0000542!4.29e-33!53;CL:0000051!4.29e-33!53;CL:0000838!3.20e-32!52;CL:0000791!3.27e-19!18;CL:0000789!3.27e-19!18;CL:0002420!3.27e-19!18;CL:0002419!3.27e-19!18;CL:0000790!3.27e-19!18;CL:0002009!2.64e-18!65;CL:0000084!3.65e-18!25;CL:0000827!3.65e-18!25;CL:0000763!6.07e-18!112;CL:0000049!6.07e-18!112;CL:0000557!2.95e-17!71;CL:0002194!1.23e-16!63;CL:0000576!1.23e-16!63;CL:0000040!1.23e-16!63;CL:0000559!1.23e-16!63;CL:0002057!4.33e-16!42;CL:0000766!1.57e-15!76;CL:0000839!2.96e-15!70;CL:0000860!2.48e-14!45;CL:0000945!3.91e-13!24;CL:0000826!3.91e-13!24;CL:0000625!1.06e-12!11;CL:0000451!8.26e-11!10;CL:0000990!9.83e-10!8;CL:0000134!4.68e-08!358;CL:0000453!1.94e-07!5;CL:0002320!2.10e-07!365;CL:0000624!4.05e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!5.02e-29!102;UBERON:0003061!5.02e-29!102;UBERON:0002193!6.58e-27!112;UBERON:0002371!1.06e-14!80;UBERON:0001474!1.04e-12!86;UBERON:0002405!1.63e-12!115;UBERON:0000178!4.83e-12!15;UBERON:0000179!4.83e-12!15;UBERON:0000463!4.83e-12!15;UBERON:0004765!6.59e-09!101;UBERON:0001434!6.59e-09!101;UBERON:0007023!7.60e-09!115;UBERON:0004177!2.45e-08!7;UBERON:0002384!4.33e-07!375
}}
}}

Revision as of 14:37, 21 May 2012


Full id: C3491_migratory_CD4_splenic_immature_xeroderma_b_lymphangiectasia



Phase1 CAGE Peaks

Hg19::chr15:45028520..45028556,+p9@TRIM69
Hg19::chr15:45028572..45028586,+p16@TRIM69
Hg19::chr2:231789941..231789975,-p1@GPR55


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
leukocyte4.70e-55140
nongranular leukocyte3.51e-51119
hematopoietic stem cell6.05e-51172
angioblastic mesenchymal cell6.05e-51172
hematopoietic cell8.53e-50182
hematopoietic oligopotent progenitor cell2.65e-48165
hematopoietic multipotent progenitor cell2.65e-48165
hematopoietic lineage restricted progenitor cell1.22e-47124
lymphocyte4.29e-3353
common lymphoid progenitor4.29e-3353
lymphoid lineage restricted progenitor cell3.20e-3252
mature alpha-beta T cell3.27e-1918
alpha-beta T cell3.27e-1918
immature T cell3.27e-1918
mature T cell3.27e-1918
immature alpha-beta T cell3.27e-1918
macrophage dendritic cell progenitor2.64e-1865
T cell3.65e-1825
pro-T cell3.65e-1825
myeloid cell6.07e-18112
common myeloid progenitor6.07e-18112
granulocyte monocyte progenitor cell2.95e-1771
monopoietic cell1.23e-1663
monocyte1.23e-1663
monoblast1.23e-1663
promonocyte1.23e-1663
CD14-positive, CD16-negative classical monocyte4.33e-1642
myeloid leukocyte1.57e-1576
myeloid lineage restricted progenitor cell2.96e-1570
classical monocyte2.48e-1445
lymphocyte of B lineage3.91e-1324
pro-B cell3.91e-1324
CD8-positive, alpha-beta T cell1.06e-1211
dendritic cell8.26e-1110
conventional dendritic cell9.83e-108
mesenchymal cell4.68e-08358
Langerhans cell1.94e-075
connective tissue cell2.10e-07365
CD4-positive, alpha-beta T cell4.05e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.02e-29102
blood island5.02e-29102
hemolymphoid system6.58e-27112
bone marrow1.06e-1480
bone element1.04e-1286
immune system1.63e-12115
blood4.83e-1215
haemolymphatic fluid4.83e-1215
organism substance4.83e-1215
skeletal element6.59e-09101
skeletal system6.59e-09101
adult organism7.60e-09115
hemopoietic organ2.45e-087
connective tissue4.33e-07375


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.