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Coexpression cluster:C543

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Full id: C543_Alveolar_Corneal_Urothelial_amniotic_Esophageal_Tracheal_esophagus



Phase1 CAGE Peaks

Hg19::chr15:41136499..41136552,-p@chr15:41136499..41136552
-
Hg19::chr15:41136586..41136725,+p1@SPINT1
Hg19::chr15:41136734..41136749,+p9@SPINT1
Hg19::chr16:67233007..67233061,+p1@ELMO3
Hg19::chr19:10697917..10697993,-p1@AP1M2
Hg19::chr19:4338783..4338834,-p1@STAP2
Hg19::chr19:50084561..50084603,+p1@PRRG2
Hg19::chr19:50084621..50084673,+p2@PRRG2
Hg19::chr1:156030937..156030983,+p1@RAB25
Hg19::chr1:156030987..156031007,+p2@RAB25
Hg19::chr1:201368707..201368760,-p3@LAD1
Hg19::chr1:26503974..26504025,+p1@CNKSR1
Hg19::chr1:27286862..27286885,-p2@C1orf172
Hg19::chr1:27286905..27286966,-p1@C1orf172
Hg19::chr20:821883..821934,+p@chr20:821883..821934
+
Hg19::chr6:42110342..42110365,-p1@C6orf132
Hg19::chrX:48916506..48916557,+p1@CCDC120


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.52e-27160
endoderm1.52e-27160
presumptive endoderm1.52e-27160
digestive system1.96e-20145
digestive tract1.96e-20145
primitive gut1.96e-20145
subdivision of digestive tract8.78e-18118
respiratory system1.90e-1474
renal system8.91e-1348
endo-epithelium1.72e-1282
anatomical space2.23e-1295
urinary system structure2.30e-1247
immaterial anatomical entity9.83e-12117
foregut6.42e-1187
orifice1.00e-1036
trunk region element1.62e-10101
epithelial bud2.16e-1037
extraembryonic membrane4.03e-1014
membranous layer4.03e-1014
organ4.48e-10503
respiratory tract6.93e-1054
thoracic cavity element2.96e-0934
thoracic cavity2.96e-0934
reproductive structure6.20e-0959
reproductive system6.20e-0959
thoracic segment organ8.51e-0935
epithelial fold1.36e-0847
oral opening1.69e-0822
organism subdivision3.73e-08264
subdivision of trunk6.47e-08112
organ part7.75e-08218
multi-cellular organism9.45e-08656
reproductive organ1.18e-0748
nephron tubule epithelium1.23e-0710
chorion1.24e-077
internal genitalia1.92e-0725
thoracic segment of trunk2.24e-0752
gland5.69e-0759
respiratory primordium7.49e-0738
endoderm of foregut7.49e-0738
embryo8.26e-07592
Disease
Ontology termp-valuen
carcinoma9.72e-20106
cell type cancer2.73e-12143
squamous cell carcinoma5.48e-1214
adenocarcinoma8.26e-0925


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
E2F1#186982.309359630531450.01224933189154410.04440808016596
MYC#460982.457544410169130.008361946486306990.032921677124568
POLR2A#5430172.147453176558072.27473247069268e-068.13320042816408e-05
TAF1#6872112.163147596658720.003152426505870830.0165503580076732
ZEB1#693587.947497420020642.25657064892169e-068.0710267809155e-05



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.