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Coexpression cluster:C2349

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Full id: C2349_Mast_CD14_Smooth_Mesenchymal_Hair_mesothelioma_papillotubular



Phase1 CAGE Peaks

Hg19::chr15:75913265..75913337,-p4@SNUPN
Hg19::chr16:27258633..27258637,+p@chr16:27258633..27258637
+
Hg19::chr19:35646092..35646138,+p2@FXYD5
Hg19::chr19:35646149..35646177,+p5@FXYD5


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


GO IDGO nameFDR corrected p-value
GO:0046588negative regulation of calcium-dependent cell-cell adhesion0.00259036853879666
GO:0046586regulation of calcium-dependent cell-cell adhesion0.00259036853879666
GO:0030033microvillus biogenesis0.006475540085248
GO:0032528microvillus organization and biogenesis0.006475540085248
GO:0000339RNA cap binding0.0072523913889013
GO:0022408negative regulation of cell-cell adhesion0.00805738235098189
GO:0045296cadherin binding0.00805738235098189
GO:0022407regulation of cell-cell adhesion0.00805738235098189
GO:0050839cell adhesion molecule binding0.00805738235098189
GO:0016339calcium-dependent cell-cell adhesion0.0122408727264318
GO:0007162negative regulation of cell adhesion0.0122408727264318
GO:0022892substrate-specific transporter activity0.0198064840396804
GO:0030155regulation of cell adhesion0.0262770403496228
GO:0005643nuclear pore0.0298227869868878
GO:0006606protein import into nucleus0.0298227869868878
GO:0046930pore complex0.0298227869868878
GO:0051170nuclear import0.0298227869868878
GO:0044453nuclear membrane part0.0318961541352686
GO:0017038protein import0.0332065413839154
GO:0031965nuclear membrane0.0341084762377736
GO:0006913nucleocytoplasmic transport0.0341084762377736
GO:0008565protein transporter activity0.0341084762377736
GO:0051169nuclear transport0.0341084762377736
GO:0016043cellular component organization and biogenesis0.0341084762377736
GO:0005635nuclear envelope0.0376325929129757
GO:0032990cell part morphogenesis0.0376325929129757
GO:0048858cell projection morphogenesis0.0376325929129757
GO:0030030cell projection organization and biogenesis0.0376325929129757
GO:0006605protein targeting0.0388204651484896
GO:0006810transport0.0413724656089171
GO:0051234establishment of localization0.0420472423208777
GO:0051179localization0.047836148453937



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
defensive cell2.17e-2348
phagocyte2.17e-2348
classical monocyte3.99e-2142
CD14-positive, CD16-negative classical monocyte3.99e-2142
somatic cell1.85e-20588
native cell2.07e-20722
myeloid lineage restricted progenitor cell3.07e-2066
granulocyte monocyte progenitor cell4.06e-2067
animal cell9.63e-20679
eukaryotic cell9.63e-20679
monopoietic cell1.40e-1959
monocyte1.40e-1959
monoblast1.40e-1959
promonocyte1.40e-1959
stem cell2.78e-19441
multi fate stem cell3.18e-19427
myeloid leukocyte5.90e-1972
somatic stem cell7.86e-19433
macrophage dendritic cell progenitor1.22e-1861
myeloid cell1.27e-15108
common myeloid progenitor1.27e-15108
mesenchymal cell1.14e-13354
connective tissue cell2.18e-13361
stuff accumulating cell4.92e-1387
vascular associated smooth muscle cell9.28e-1132
motile cell1.11e-09386
smooth muscle cell3.94e-0943
smooth muscle myoblast3.94e-0943
muscle cell1.60e-0855
muscle precursor cell8.45e-0858
myoblast8.45e-0858
multi-potent skeletal muscle stem cell8.45e-0858
contractile cell2.19e-0759
mesodermal cell7.12e-07121
fibroblast9.67e-0776


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
FOS#235336.74846648167080.005032452776317940.0234614916304736
THAP1#55145215.68457230142570.005840469678357920.0262444201332942



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.