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Coexpression cluster:C3846

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Full id: C3846_astrocytoma_alveolar_mesothelioma_small_mucinous_Pericytes_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:110198761..110198791,+p4@GSTM4
Hg19::chr1:110198920..110198942,+p3@GSTM4
Hg19::chr1:110198944..110198996,+p2@GSTM4


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.59e-22115
central nervous system3.61e-1982
regional part of nervous system4.68e-1894
nervous system4.68e-1894
brain2.57e-1769
future brain2.57e-1769
neural tube3.70e-1757
neural rod3.70e-1757
future spinal cord3.70e-1757
neural keel3.70e-1757
regional part of brain1.31e-1659
neurectoderm1.57e-1590
neural plate1.08e-1486
presumptive neural plate1.08e-1486
multi-tissue structure1.41e-13347
regional part of forebrain7.37e-1241
forebrain7.37e-1241
future forebrain7.37e-1241
organ1.09e-11511
ectoderm1.49e-11173
presumptive ectoderm1.49e-11173
anterior neural tube1.85e-1142
head3.09e-11123
telencephalon5.41e-1134
anterior region of body7.42e-11129
craniocervical region7.42e-11129
ectoderm-derived structure7.69e-11169
organism subdivision9.24e-11365
multi-cellular organism1.14e-10659
regional part of telencephalon1.55e-1033
gray matter1.90e-1034
brain grey matter1.90e-1034
cerebral hemisphere3.64e-1032
pre-chordal neural plate1.22e-0961
anatomical cluster2.97e-08286
embryo6.41e-08612
cerebral cortex1.77e-0725
pallium1.77e-0725
anatomical group3.10e-07626
posterior neural tube3.33e-0715
chordal neural plate3.33e-0715
anatomical system3.47e-07625
germ layer7.18e-07604
embryonic tissue7.18e-07604
presumptive structure7.18e-07604
epiblast (generic)7.18e-07604
embryonic structure7.46e-07605
developing anatomical structure7.46e-07605
regional part of cerebral cortex8.73e-0722
organ part9.57e-07219


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
CTCF#1066435.360256373075030.0064925092527670.0279478680178771
CTCFL#140690319.74647435897440.0001298372005551160.0017177688610053
E2F6#187635.017155731697390.00791769806886330.0322258951135625
EBF1#187938.9064668465690.00141523283560980.00915204347481439
ELF1#199734.258097958807540.01295179875054610.0462373238662889
GABPB1#255337.067683836182170.002832212825417420.0154147415328454
HNF4A#3172323.13229036295378.07584663437677e-050.00122788374821324
HNF4G#3174328.75342252644684.20470658818262e-050.000756738499678106
IRF1#365937.63716375356390.002244692747297240.0128105719035506
MYC#460935.22228187160940.007020843755740150.0294548847515765
NFKB1#479035.488063424193840.006049381815655430.026965061350629
PAX5#507936.669565531177830.003370290999677260.017293397942188
REST#597839.650028716128020.001112636247114590.00767621991097904
SIN3A#2594235.408884726815140.006318961977991520.0276811404731117
SP1#666735.69838137814090.005403962701712170.0246552994890619
ZBTB7A#5134137.35190930787590.002516255860282270.0140217290466343



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.