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|full_id=C3056_epidermoid_Renal_anaplastic_clear_Iris_ductal_Retinal
|full_id=C3056_epidermoid_Renal_anaplastic_clear_Iris_ductal_Retinal
|id=C3056
|id=C3056
|ontology_enrichment_celltype=CL:1000497!2.41e-08!18;CL:0002518!2.41e-08!18;CL:0000077!3.73e-08!19;CL:1000507!3.33e-07!12;CL:1000494!3.33e-07!12;CL:1000449!6.53e-07!16
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003075!4.78e-11!86;UBERON:0007284!4.78e-11!86;UBERON:0002346!8.78e-11!90;UBERON:0002113!1.83e-10!27;UBERON:0003918!1.83e-10!27;UBERON:0005095!1.83e-10!27;UBERON:0007687!1.83e-10!27;UBERON:0000489!2.08e-10!32;UBERON:0000475!8.60e-10!365;UBERON:0007625!8.69e-10!11;UBERON:0000058!7.34e-09!26;UBERON:0005743!1.50e-08!86;UBERON:0006554!2.10e-08!44;UBERON:0000073!2.50e-08!94;UBERON:0001016!2.50e-08!94;UBERON:0000080!3.83e-08!18;UBERON:0002120!3.83e-08!18;UBERON:0004875!3.83e-08!18;UBERON:0005721!3.83e-08!18;UBERON:0005754!3.83e-08!18;UBERON:0007297!3.83e-08!18;UBERON:0004876!5.32e-08!20;UBERON:0001008!5.54e-08!45;UBERON:0000064!9.23e-08!219;UBERON:0000481!1.09e-07!347;UBERON:0000119!1.13e-07!312;UBERON:0003056!1.37e-07!61;UBERON:0006555!1.59e-07!17;UBERON:0005103!1.59e-07!17;UBERON:0000083!1.59e-07!17;UBERON:0009201!1.59e-07!17;UBERON:0004819!1.59e-07!17;UBERON:0006553!1.59e-07!17;UBERON:0003074!1.59e-07!17;UBERON:0003060!1.59e-07!17;UBERON:0002417!1.62e-07!61;UBERON:0000916!1.62e-07!61;UBERON:0000483!2.20e-07!309;UBERON:0003887!2.24e-07!21;UBERON:0000970!2.28e-07!20;UBERON:0009773!3.33e-07!12;UBERON:0001231!3.33e-07!12;UBERON:0004810!3.33e-07!12;UBERON:0000062!3.42e-07!511;UBERON:0000955!3.92e-07!69;UBERON:0006238!3.92e-07!69;UBERON:0000033!4.11e-07!123;UBERON:0004211!6.53e-07!16;UBERON:0001285!6.53e-07!16;UBERON:0007684!6.53e-07!16;UBERON:0003220!6.53e-07!16;UBERON:0004208!6.53e-07!16;UBERON:0000019!7.73e-07!19;UBERON:0000047!7.73e-07!19;UBERON:0004088!7.73e-07!19;UBERON:0003072!7.73e-07!19;UBERON:0003071!7.73e-07!19;UBERON:0004128!7.73e-07!19;UBERON:0004175!7.93e-07!25;UBERON:0001017!8.13e-07!82;UBERON:0000020!9.51e-07!23;UBERON:0002104!9.75e-07!21
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Revision as of 14:31, 21 May 2012


Full id: C3056_epidermoid_Renal_anaplastic_clear_Iris_ductal_Retinal



Phase1 CAGE Peaks

Hg19::chr10:91043420..91043437,+p1@ENST00000444849
Hg19::chr10:91043443..91043456,+p2@ENST00000444849
Hg19::chr10:91043477..91043497,+p1@ENST00000354541


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
kidney cell2.41e-0818
kidney epithelial cell2.41e-0818
mesothelial cell3.73e-0819
kidney tubule cell3.33e-0712
nephron tubule epithelial cell3.33e-0712
epithelial cell of nephron6.53e-0716
Uber Anatomy
Ontology termp-valuen
neural plate4.78e-1186
presumptive neural plate4.78e-1186
neurectoderm8.78e-1190
kidney1.83e-1027
kidney mesenchyme1.83e-1027
kidney rudiment1.83e-1027
kidney field1.83e-1027
cavitated compound organ2.08e-1032
organism subdivision8.60e-10365
pigment epithelium of eye8.69e-1011
duct7.34e-0926
urinary system structure2.10e-0844
regional part of nervous system2.50e-0894
nervous system2.50e-0894
mesonephros3.83e-0818
pronephros3.83e-0818
nephrogenic cord3.83e-0818
pronephric mesoderm3.83e-0818
rostral part of nephrogenic cord3.83e-0818
presumptive pronephric mesoderm3.83e-0818
urogenital ridge5.32e-0820
renal system5.54e-0845
organ part9.23e-08219
multi-tissue structure1.09e-07347
cell layer1.13e-07312
pre-chordal neural plate1.37e-0761
excretory tube1.59e-0717
mesonephric epithelium1.59e-0717
mesonephric tubule1.59e-0717
nephric duct1.59e-0717
kidney epithelium1.59e-0717
renal duct1.59e-0717
mesonephric duct1.59e-0717
pronephric duct1.59e-0717
abdominal segment of trunk1.62e-0761
abdomen1.62e-0761
epithelium2.20e-07309
intraembryonic coelom2.24e-0721
eye2.28e-0720
renal tubule3.33e-0712
nephron tubule3.33e-0712
nephron tubule epithelium3.33e-0712
organ3.42e-07511
brain3.92e-0769
future brain3.92e-0769
head4.11e-07123
nephron epithelium6.53e-0716
nephron6.53e-0716
uriniferous tubule6.53e-0716
metanephric mesenchyme6.53e-0716
nephrogenic mesenchyme6.53e-0716
camera-type eye7.73e-0719
simple eye7.73e-0719
ocular region7.73e-0719
optic cup7.73e-0719
eye primordium7.73e-0719
optic vesicle7.73e-0719
internal genitalia7.93e-0725
central nervous system8.13e-0782
sense organ9.51e-0723
visual system9.75e-0721


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.