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Coexpression cluster:C1224

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Full id: C1224_CD4_xeroderma_splenic_CD8_Peripheral_Natural_lymph



Phase1 CAGE Peaks

Hg19::chr16:84801852..84801877,+p@chr16:84801852..84801877
+
Hg19::chr2:242051921..242051933,-p15@PASK
Hg19::chr2:242051966..242051973,-p14@PASK
Hg19::chr2:242051975..242051994,-p2@PASK
Hg19::chr2:242051995..242052016,-p7@PASK
Hg19::chr2:242052022..242052034,-p11@PASK
Hg19::chr2:242052089..242052103,-p9@PASK


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
leukocyte2.15e-31140
nongranular leukocyte1.57e-28119
hematopoietic stem cell2.39e-24172
angioblastic mesenchymal cell2.39e-24172
hematopoietic lineage restricted progenitor cell4.18e-24124
hematopoietic oligopotent progenitor cell2.22e-22165
hematopoietic multipotent progenitor cell2.22e-22165
hematopoietic cell3.49e-22182
lymphoid lineage restricted progenitor cell1.29e-1952
lymphocyte6.39e-1953
common lymphoid progenitor6.39e-1953
mature alpha-beta T cell2.71e-1518
alpha-beta T cell2.71e-1518
immature T cell2.71e-1518
mature T cell2.71e-1518
immature alpha-beta T cell2.71e-1518
T cell5.42e-1325
pro-T cell5.42e-1325
myeloid leukocyte1.23e-1176
CD8-positive, alpha-beta T cell3.34e-1111
CD14-positive, CD16-negative classical monocyte1.30e-1042
classical monocyte2.22e-1045
monopoietic cell5.06e-0963
monocyte5.06e-0963
monoblast5.06e-0963
promonocyte5.06e-0963
macrophage dendritic cell progenitor5.79e-0965
granulocyte monocyte progenitor cell1.15e-0771
myeloid lineage restricted progenitor cell2.05e-0770
myeloid cell2.32e-07112
common myeloid progenitor2.32e-07112
CD4-positive, alpha-beta T cell4.41e-076
granulocyte6.09e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.68e-15102
blood island5.68e-15102
hemolymphoid system4.00e-14112
blood3.26e-1015
haemolymphatic fluid3.26e-1015
organism substance3.26e-1015


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#53335624.31667580309181.29931738009616e-089.60363820664283e-07
EBF1#187967.634114439916291.2666377582912e-050.000312143418683752
MEF2A#4205616.06562649398061.53846883349817e-078.6292237648612e-06
MEF2C#4208635.40973242224921.3745684456669e-091.23438137486677e-07
NFKB1#479064.704054363594720.000216115061401970.00247786155426066
SP1#666764.884326895549340.0001736361122290910.00211331801947255



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.