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Coexpression cluster:C4412

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Full id: C4412_argyrophil_rectum_testis_testicular_iPS_choriocarcinoma_small



Phase1 CAGE Peaks

Hg19::chr4:40751927..40751995,+p1@NSUN7
Hg19::chr4:40752000..40752023,+p3@NSUN7
Hg19::chr4:40752184..40752240,+p2@NSUN7


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>


Cell Type
Ontology termp-valuen
epithelial cell7.93e-12253
Uber Anatomy
Ontology termp-valuen
organ part1.54e-09218
organ system subdivision2.79e-08223
anatomical cluster5.03e-08373
anatomical space5.27e-0895
intestine5.95e-0817
gastrointestinal system7.92e-0825
endoderm-derived structure1.05e-07160
endoderm1.05e-07160
presumptive endoderm1.05e-07160
embryo1.39e-07592
organ segment1.73e-0798
adult organism2.18e-07114
organ3.15e-07503
multi-tissue structure4.28e-07342
excretory tube4.96e-0716
kidney epithelium4.96e-0716
cavitated compound organ5.39e-0731
eye5.70e-0721
visual system5.70e-0721
multi-cellular organism6.63e-07656
digestive system7.12e-07145
digestive tract7.12e-07145
primitive gut7.12e-07145
male reproductive organ7.18e-0711
sense organ8.01e-0724
sensory system8.01e-0724
entire sense organ system8.01e-0724
pigment epithelium of eye9.51e-0711
Disease
Ontology termp-valuen
carcinoma3.31e-12106
cell type cancer4.89e-10143


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
CHD2#1106310.34402283411690.0009033701102746880.00662270608921649
E2F1#186934.907389214879320.008460985347239390.0326917073133679
EBF1#187938.9064668465690.00141523283560980.00918103622077473
JUND#372736.994663941871030.002921845042734990.0157336723082341
MYC#460935.22228187160940.007020843755740150.0295569937522471
NANOG#79923329.24477848101273.99627955670032e-050.000739750869589197
SP1#666735.69838137814090.005403962701712170.0247504477745962
TCF12#6938310.63446490218640.0008313523990202070.00631091824402321
ZBTB33#10009331.66472502998123.14815888737575e-050.000634608311211419
ZEB1#6935316.88843201754390.0002075486917327580.00243470491024121



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.