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Coexpression cluster:C2705

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Full id: C2705_kidney_brain_occipital_duodenum_Neurons_Renal_temporal



Phase1 CAGE Peaks

Hg19::chr2:73144617..73144654,+p1@EMX1
Hg19::chr2:73144668..73144679,+p5@EMX1
Hg19::chr2:73144683..73144697,+p3@EMX1
Hg19::chr2:73144739..73144750,+p4@EMX1


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
neuronal stem cell1.04e-118
neural cell2.04e-0925
neuron3.55e-096
neuroblast3.55e-096
electrically signaling cell3.55e-096
Uber Anatomy
Ontology termp-valuen
cerebral cortex4.64e-3625
pallium4.64e-3625
regional part of cerebral cortex4.26e-3222
cerebral hemisphere1.34e-3132
telencephalon2.65e-3134
regional part of telencephalon7.95e-3033
neocortex1.13e-2920
gray matter1.26e-2834
brain grey matter1.26e-2834
central nervous system9.74e-2882
regional part of forebrain4.59e-2641
forebrain4.59e-2641
future forebrain4.59e-2641
anterior neural tube3.20e-2542
regional part of nervous system5.34e-2294
nervous system5.34e-2294
brain1.25e-1969
future brain1.25e-1969
neural tube1.65e-1857
neural rod1.65e-1857
future spinal cord1.65e-1857
neural keel1.65e-1857
regional part of brain1.48e-1759
pre-chordal neural plate1.00e-1561
neural plate9.75e-1486
presumptive neural plate9.75e-1486
neurectoderm1.16e-1290
ectoderm-derived structure9.72e-11169
gyrus1.88e-106
ectoderm3.56e-10173
presumptive ectoderm3.56e-10173
temporal lobe3.71e-107
head1.56e-09123
occipital lobe2.30e-095
anterior region of body3.82e-09129
craniocervical region3.82e-09129
parietal lobe4.27e-095
adult organism2.79e-08115
limbic system3.32e-085
Disease
Ontology termp-valuen
carcinoma3.51e-07106


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
E2F6#187645.017155731697390.00157802193473060.00998104607808436
JUND#372746.994663941871030.000417684217818580.00392112557525885
NFKB1#479045.488063424193840.001102199566301980.00768647305722571
SIN3A#2594245.408884726815140.001168172384885160.00797455753350028
SP1#666745.69838137814090.0009482606065333980.00685081554273254
SUZ12#23512450.11578091106291.5827390373096e-078.8348306957551e-06
TAF1#687243.343046285745290.008005664898701650.0322795010561154
YY1#752844.911170749853860.00171871838055440.0106986070417643
ZEB1#6935416.88843201754391.22862303393937e-050.000304933842779453



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.