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Coexpression cluster:C2605

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Full id: C2605_Reticulocytes_liver_Hepatocyte_retina_left_heart_gastrointestinal



Phase1 CAGE Peaks

Hg19::chr1:95582881..95582994,+p1@TMEM56
Hg19::chr1:95583232..95583264,+p3@RWDD3
p3@TMEM56
Hg19::chr3:142682505..142682521,-p2@PAQR9
Hg19::chr7:100239132..100239196,-p3@TFR2


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:0004998transferrin receptor activity0.00865393104790558



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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism4.54e-49115
neural plate6.18e-2586
presumptive neural plate6.18e-2586
neural tube3.25e-2457
neural rod3.25e-2457
future spinal cord3.25e-2457
neural keel3.25e-2457
central nervous system5.92e-2382
regional part of nervous system7.18e-2394
nervous system7.18e-2394
neurectoderm1.25e-2290
brain3.65e-2269
future brain3.65e-2269
regional part of brain7.73e-2059
anterior neural tube9.65e-2042
regional part of forebrain1.42e-1941
forebrain1.42e-1941
future forebrain1.42e-1941
pre-chordal neural plate5.59e-1861
telencephalon1.66e-1734
gray matter3.31e-1734
brain grey matter3.31e-1734
head4.85e-17123
regional part of telencephalon6.22e-1733
cerebral hemisphere7.45e-1732
anterior region of body1.63e-16129
craniocervical region1.63e-16129
ectoderm-derived structure8.21e-16169
multi-tissue structure1.01e-15347
ectoderm1.00e-14173
presumptive ectoderm1.00e-14173
regional part of cerebral cortex9.23e-1422
cerebral cortex5.16e-1325
pallium5.16e-1325
neocortex1.19e-1220
organ part5.88e-12219
anatomical cluster5.01e-10286
subdivision of digestive tract5.89e-10129
endodermal part of digestive tract5.89e-10129
digestive system9.46e-10155
digestive tract9.46e-10155
primitive gut9.46e-10155
organism subdivision1.59e-08365
organ2.31e-08511
anatomical conduit4.17e-08241
mixed endoderm/mesoderm-derived structure7.19e-08130
endoderm-derived structure7.95e-08169
endoderm7.95e-08169
presumptive endoderm7.95e-08169
tube8.93e-08194
epithelium3.98e-07309
cell layer9.97e-07312
Disease
Ontology termp-valuen
carcinoma5.91e-13106
cell type cancer8.25e-12143
cancer1.36e-07235
disease of cellular proliferation2.50e-07239


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
CCNT2#90546.336201576962630.0006203100587215640.00512617203852045
E2F6#187645.017155731697390.00157802193473060.00997621264172694
HEY1#2346244.040111043105710.00375304636917980.0186250610477914
HMGN3#932436.133910792512940.006640696683324720.0283011393499449
TAF1#687243.343046285745290.008005664898701650.0322558402976545
ZBTB7A#5134135.513931980906920.009038352821081090.0342509626371875



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.