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Coexpression cluster:C1921: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000119!3.24e-31!312;UBERON:0000481!2.37e-30!347;UBERON:0000483!4.19e-30!309;UBERON:0000475!4.24e-26!365;UBERON:0004111!1.15e-25!241;UBERON:0000477!3.02e-24!286;UBERON:0000924!5.01e-22!173;UBERON:0006601!5.01e-22!173;UBERON:0004121!1.27e-21!169;UBERON:0000468!1.45e-21!659;UBERON:0000025!1.55e-21!194;UBERON:0000922!2.62e-21!612;UBERON:0000033!7.11e-21!123;UBERON:0005743!8.65e-21!86;UBERON:0002346!9.16e-20!90;UBERON:0000153!9.42e-20!129;UBERON:0007811!9.42e-20!129;UBERON:0003075!1.55e-19!86;UBERON:0007284!1.55e-19!86;UBERON:0000073!1.69e-19!94;UBERON:0001016!1.69e-19!94;UBERON:0002050!9.31e-19!605;UBERON:0005423!9.31e-19!605;UBERON:0001017!1.36e-18!82;UBERON:0000923!2.51e-18!604;UBERON:0005291!2.51e-18!604;UBERON:0006598!2.51e-18!604;UBERON:0002532!2.51e-18!604;UBERON:0000467!5.89e-18!625;UBERON:0000480!1.19e-17!626;UBERON:0000955!1.00e-14!69;UBERON:0006238!1.00e-14!69;UBERON:0000064!3.70e-14!219;UBERON:0005256!1.03e-13!143;UBERON:0002616!1.31e-13!59;UBERON:0003056!1.50e-13!61;UBERON:0000062!1.94e-13!511;UBERON:0000466!7.30e-13!126;UBERON:0001049!1.45e-12!57;UBERON:0005068!1.45e-12!57;UBERON:0006241!1.45e-12!57;UBERON:0007135!1.45e-12!57;UBERON:0001048!3.16e-11!168;UBERON:0003914!2.44e-10!118;UBERON:0003104!3.88e-10!238;UBERON:0009142!3.88e-10!238;UBERON:0002100!4.38e-10!216;UBERON:0000464!7.49e-10!104;UBERON:0007023!9.56e-10!115;UBERON:0003103!2.12e-09!69;UBERON:0005177!2.21e-09!107;UBERON:0002553!2.60e-09!70;UBERON:0003886!4.83e-09!63;UBERON:0001032!6.85e-09!24;UBERON:0004456!6.85e-09!24;UBERON:0000020!1.87e-08!23;UBERON:0003064!2.22e-08!37;UBERON:0002104!3.73e-08!21;UBERON:0002780!4.32e-08!41;UBERON:0001890!4.32e-08!41;UBERON:0006240!4.32e-08!41;UBERON:0003080!5.89e-08!42;UBERON:0006555!6.88e-08!17;UBERON:0005103!6.88e-08!17;UBERON:0000083!6.88e-08!17;UBERON:0009201!6.88e-08!17;UBERON:0004819!6.88e-08!17;UBERON:0006553!6.88e-08!17;UBERON:0003074!6.88e-08!17;UBERON:0003060!6.88e-08!17;UBERON:0000080!7.09e-08!18;UBERON:0002120!7.09e-08!18;UBERON:0004875!7.09e-08!18;UBERON:0005721!7.09e-08!18;UBERON:0005754!7.09e-08!18;UBERON:0007297!7.09e-08!18;UBERON:0000970!1.02e-07!20;UBERON:0004211!1.47e-07!16;UBERON:0001285!1.47e-07!16;UBERON:0007684!1.47e-07!16;UBERON:0003220!1.47e-07!16;UBERON:0004208!1.47e-07!16;UBERON:0003887!2.45e-07!21;UBERON:0000019!3.03e-07!19;UBERON:0000047!3.03e-07!19;UBERON:0004088!3.03e-07!19;UBERON:0003072!3.03e-07!19;UBERON:0003071!3.03e-07!19;UBERON:0004128!3.03e-07!19;UBERON:0001456!5.10e-07!21;UBERON:0005172!5.55e-07!55;UBERON:0005173!5.55e-07!55;UBERON:0000490!7.74e-07!138;UBERON:0004876!8.06e-07!20;UBERON:0007625!8.87e-07!11;UBERON:0000058!9.35e-07!26
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}}
}}

Revision as of 17:47, 8 August 2012


Full id: C1921_small_Renal_Ciliary_Astrocyte_Lens_Meningeal_maxillary



Phase1 CAGE Peaks

Hg19::chr3:139258363..139258374,-p4@RBP1
Hg19::chr3:139258382..139258393,-p5@RBP1
Hg19::chr3:139258420..139258434,-p3@RBP1
Hg19::chr3:139258443..139258485,-p1@RBP1
Hg19::chr3:139258521..139258589,-p2@RBP1


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
embryonic cell1.47e-13248
epithelial cell of nephron1.47e-0716
electrically responsive cell2.19e-0760
electrically active cell2.19e-0760
contractile cell2.78e-0759
ectodermal cell9.75e-0771
Uber Anatomy
Ontology termp-valuen
cell layer3.24e-31312
multi-tissue structure2.37e-30347
epithelium4.19e-30309
organism subdivision4.24e-26365
anatomical conduit1.15e-25241
anatomical cluster3.02e-24286
ectoderm5.01e-22173
presumptive ectoderm5.01e-22173
ectoderm-derived structure1.27e-21169
multi-cellular organism1.45e-21659
tube1.55e-21194
embryo2.62e-21612
head7.11e-21123
neurectoderm9.16e-2090
anterior region of body9.42e-20129
craniocervical region9.42e-20129
neural plate1.55e-1986
presumptive neural plate1.55e-1986
regional part of nervous system1.69e-1994
nervous system1.69e-1994
embryonic structure9.31e-19605
developing anatomical structure9.31e-19605
central nervous system1.36e-1882
germ layer2.51e-18604
embryonic tissue2.51e-18604
presumptive structure2.51e-18604
epiblast (generic)2.51e-18604
anatomical system5.89e-18625
anatomical group1.19e-17626
brain1.00e-1469
future brain1.00e-1469
organ part3.70e-14219
trunk mesenchyme1.03e-13143
regional part of brain1.31e-1359
pre-chordal neural plate1.50e-1361
organ1.94e-13511
immaterial anatomical entity7.30e-13126
neural tube1.45e-1257
neural rod1.45e-1257
future spinal cord1.45e-1257
neural keel1.45e-1257
primordium3.16e-11168
epithelial tube2.44e-10118
mesenchyme3.88e-10238
entire embryonic mesenchyme3.88e-10238
trunk4.38e-10216
anatomical space7.49e-10104
adult organism9.56e-10115
compound organ2.12e-0969
trunk region element2.21e-09107
anatomical cavity2.60e-0970
body cavity precursor4.83e-0963
sensory system6.85e-0924
entire sense organ system6.85e-0924
sense organ1.87e-0823
intermediate mesoderm2.22e-0837
visual system3.73e-0821
regional part of forebrain4.32e-0841
forebrain4.32e-0841
future forebrain4.32e-0841
anterior neural tube5.89e-0842
excretory tube6.88e-0817
mesonephric epithelium6.88e-0817
mesonephric tubule6.88e-0817
nephric duct6.88e-0817
kidney epithelium6.88e-0817
renal duct6.88e-0817
mesonephric duct6.88e-0817
pronephric duct6.88e-0817
mesonephros7.09e-0818
pronephros7.09e-0818
nephrogenic cord7.09e-0818
pronephric mesoderm7.09e-0818
rostral part of nephrogenic cord7.09e-0818
presumptive pronephric mesoderm7.09e-0818
eye1.02e-0720
nephron epithelium1.47e-0716
nephron1.47e-0716
uriniferous tubule1.47e-0716
metanephric mesenchyme1.47e-0716
nephrogenic mesenchyme1.47e-0716
intraembryonic coelom2.45e-0721
camera-type eye3.03e-0719
simple eye3.03e-0719
ocular region3.03e-0719
optic cup3.03e-0719
eye primordium3.03e-0719
optic vesicle3.03e-0719
face5.10e-0721
abdomen element5.55e-0755
abdominal segment element5.55e-0755
unilaminar epithelium7.74e-07138


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.

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