Personal tools

Coexpression cluster:C4032

From FANTOM5_SSTAR

Revision as of 15:37, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4032_CD4_Dendritic_Natural_CD8_CD19_blood_thymus



Phase1 CAGE Peaks

Hg19::chr20:37435934..37435945,-p@chr20:37435934..37435945
-
Hg19::chr9:100864441..100864454,+p@chr9:100864441..100864454
+
Hg19::chr9:100864462..100864485,+p@chr9:100864462..100864485
+


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
lymphocyte2.78e-4253
common lymphoid progenitor2.78e-4253
nucleate cell1.85e-4055
lymphoid lineage restricted progenitor cell3.45e-4052
mature alpha-beta T cell7.97e-3718
alpha-beta T cell7.97e-3718
immature T cell7.97e-3718
mature T cell7.97e-3718
immature alpha-beta T cell7.97e-3718
T cell5.68e-2925
pro-T cell5.68e-2925
leukocyte9.57e-27136
nongranular leukocyte4.90e-24115
hematopoietic stem cell4.92e-21168
angioblastic mesenchymal cell4.92e-21168
CD4-positive, alpha-beta T cell5.68e-206
hematopoietic cell1.87e-19177
CD8-positive, alpha-beta T cell3.31e-1711
hematopoietic lineage restricted progenitor cell7.16e-17120
hematopoietic oligopotent progenitor cell1.15e-14161
hematopoietic multipotent progenitor cell1.15e-14161
natural killer cell4.90e-113
pro-NK cell4.90e-113
plasmacytoid dendritic cell5.42e-113
naive T cell7.52e-113
single nucleate cell5.99e-103
mononuclear cell5.99e-103
lymphocyte of B lineage2.00e-0824
pro-B cell2.00e-0824
regulatory T cell1.33e-072
CD4-positive, CD25-positive, alpha-beta regulatory T cell1.33e-072
naive regulatory T cell1.33e-072
thymocyte2.37e-072
double negative thymocyte2.37e-072
double-positive, alpha-beta thymocyte2.37e-072
DN4 thymocyte2.37e-072
DN1 thymic pro-T cell2.37e-072
DN2 thymocyte2.37e-072
DN3 thymocyte2.37e-072
immature single positive thymocyte2.37e-072
early T lineage precursor2.37e-072
Uber Anatomy
Ontology termp-valuen
thymus4.34e-134
hemolymphoid system gland4.34e-134
thymic region4.34e-134
pharyngeal gland4.34e-134
thymus primordium4.34e-134
hemopoietic organ4.64e-117
immune organ4.64e-117
pharyngeal epithelium9.84e-096
chordate pharynx1.42e-0710
pharyngeal region of foregut1.42e-0710
pharynx7.43e-0711


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
BCL11A#53335218.91297006907140.003639406248379680.0183896632238872
IRF4#3662214.60967512449610.006056122473217890.0268415962901207
MEF2A#4205212.4954872730960.008235029478029740.0324881291752332
NFKB1#479035.488063424193840.006049381815655430.0269904044534022
PAX5#507936.669565531177830.003370290999677260.0173112586295821
TCF12#6938310.63446490218640.0008313523990202070.0062985573595409



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.