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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 organism1.07e-52114
organ system subdivision5.43e-33223
neural tube9.89e-3256
neural rod9.89e-3256
future spinal cord9.89e-3256
neural keel9.89e-3256
regional part of nervous system6.81e-3053
regional part of brain6.81e-3053
central nervous system1.36e-2981
neural plate7.90e-2982
presumptive neural plate7.90e-2982
brain2.92e-2868
future brain2.92e-2868
regional part of forebrain1.00e-2741
forebrain1.00e-2741
anterior neural tube1.00e-2741
future forebrain1.00e-2741
nervous system6.47e-2789
neurectoderm2.64e-2686
telencephalon3.04e-2534
brain grey matter6.92e-2534
gray matter6.92e-2534
cerebral hemisphere3.71e-2432
pre-chordal neural plate6.16e-2461
regional part of telencephalon7.04e-2432
ecto-epithelium1.38e-20104
anatomical cluster2.12e-20373
regional part of cerebral cortex1.38e-1922
cerebral cortex1.53e-1825
pallium1.53e-1825
structure with developmental contribution from neural crest2.23e-18132
neocortex5.26e-1820
multi-tissue structure4.85e-17342
ectoderm-derived structure1.52e-15171
ectoderm1.52e-15171
presumptive ectoderm1.52e-15171
organ part6.43e-12218
tube2.08e-11192
anatomical conduit4.26e-11240
subdivision of digestive tract1.12e-10118
organ2.90e-10503
digestive system1.60e-08145
digestive tract1.60e-08145
primitive gut1.60e-08145
embryo2.01e-08592
basal ganglion2.41e-089
nuclear complex of neuraxis2.41e-089
aggregate regional part of brain2.41e-089
collection of basal ganglia2.41e-089
cerebral subcortex2.41e-089
epithelium7.46e-08306
neural nucleus8.80e-089
nucleus of brain8.80e-089
developing anatomical structure1.57e-07581
cell layer1.70e-07309
temporal lobe7.16e-076
telencephalic nucleus7.83e-077
endoderm-derived structure8.84e-07160
endoderm8.84e-07160
presumptive endoderm8.84e-07160
Disease
Ontology termp-valuen
carcinoma3.55e-08106


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.