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Coexpression cluster:C3899

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Full id: C3899_acute_Burkitt_diffuse_myelodysplastic_eye_occipital_brain



Phase1 CAGE Peaks

Hg19::chr1:167298384..167298412,+p3@POU2F1
Hg19::chr1:167298425..167298440,+p8@POU2F1
Hg19::chr1:167298449..167298461,+p9@POU2F1


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
central nervous system1.90e-3982
neural tube6.65e-3757
neural rod6.65e-3757
future spinal cord6.65e-3757
neural keel6.65e-3757
cerebral hemisphere2.57e-3632
telencephalon3.40e-3634
gray matter1.52e-3534
brain grey matter1.52e-3534
regional part of forebrain5.47e-3541
forebrain5.47e-3541
future forebrain5.47e-3541
regional part of telencephalon5.73e-3533
anterior neural tube6.67e-3442
regional part of nervous system1.67e-3394
nervous system1.67e-3394
brain3.88e-3369
future brain3.88e-3369
regional part of brain9.78e-3259
cerebral cortex3.34e-2725
pallium3.34e-2725
neural plate2.96e-2586
presumptive neural plate2.96e-2586
neurectoderm1.07e-2490
neocortex3.84e-2420
regional part of cerebral cortex4.31e-2422
adult organism1.73e-23115
pre-chordal neural plate4.01e-2361
anterior region of body2.07e-17129
craniocervical region2.07e-17129
head2.15e-16123
ectoderm-derived structure4.08e-13169
ectoderm4.12e-13173
presumptive ectoderm4.12e-13173
nucleus of brain1.05e-099
neural nucleus1.05e-099
gyrus1.77e-096
occipital lobe1.75e-085
basal ganglion3.96e-089
nuclear complex of neuraxis3.96e-089
aggregate regional part of brain3.96e-089
collection of basal ganglia3.96e-089
cerebral subcortex3.96e-089
parietal lobe5.30e-085
telencephalic nucleus6.06e-087
corpus striatum2.59e-074
striatum2.59e-074
ventral part of telencephalon2.59e-074
future corpus striatum2.59e-074
temporal lobe2.78e-077
Disease
Ontology termp-valuen
hematologic cancer6.10e-1351
immune system cancer6.10e-1351
myeloid leukemia4.78e-0831
leukemia8.12e-0839
lymphoma3.47e-0710


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
BCL11A#53335328.36945510360714.37778126761649e-050.000777966816077247
NFKB1#479035.488063424193840.006049381815655430.0269731199011757
PAX5#507936.669565531177830.003370290999677260.0173001976661405
POU2F2#545239.106124057742520.001324165192682130.00882599327069557
TCF12#6938310.63446490218640.0008313523990202070.00629627361865637



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.