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Coexpression cluster:C3999: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190259815074037!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00660878894276956!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325760100523606!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322673925396657!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321039171498412!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046286371123333!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00898360814188848!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388280279686133!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128224835002449!NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324813276967926!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246107272901831!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246822557773164!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00375374437427576!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248417416057218!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616337752981797!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.01403820757436
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190259815074037!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00660878894276956!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325760100523606!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322673925396657!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321039171498412!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046286371123333!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00898360814188848!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388280279686133!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128224835002449!NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324813276967926!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246107272901831!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246822557773164!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00375374437427576!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248417416057218!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616337752981797!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.01403820757436
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}}
}}

Revision as of 16:29, 26 November 2012


Full id: C3999_anaplastic_Fibroblast_putamen_caudate_eye_frontal_testis



Phase1 CAGE Peaks

Hg19::chr1:85155895..85155909,-p5@SSX2IP
Hg19::chr1:85155912..85155935,-p3@SSX2IP
Hg19::chr1:85155939..85155984,-p2@SSX2IP


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
regional part of forebrain1.70e-1941
forebrain1.70e-1941
anterior neural tube1.70e-1941
future forebrain1.70e-1941
cerebral hemisphere1.08e-1832
central nervous system3.15e-1881
nervous system1.51e-1789
telencephalon1.81e-1734
regional part of telencephalon4.24e-1732
brain1.10e-1668
future brain1.10e-1668
brain grey matter1.61e-1534
gray matter1.61e-1534
cerebral cortex2.44e-1525
pallium2.44e-1525
regional part of nervous system2.89e-1553
regional part of brain2.89e-1553
organ system subdivision3.82e-15223
regional part of cerebral cortex8.34e-1422
neural tube8.93e-1456
neural rod8.93e-1456
future spinal cord8.93e-1456
neural keel8.93e-1456
pre-chordal neural plate2.58e-1361
neocortex8.11e-1320
ectoderm-derived structure6.43e-11171
ectoderm6.43e-11171
presumptive ectoderm6.43e-11171
neural plate1.26e-1082
presumptive neural plate1.26e-1082
neurectoderm4.38e-1086
ecto-epithelium1.35e-09104
structure with developmental contribution from neural crest3.08e-07132
adult organism4.40e-07114
Disease
Ontology termp-valuen
disease of cellular proliferation9.23e-12239
cancer1.09e-10235
cell type cancer5.18e-08143
carcinoma8.99e-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#90536.336201576962630.003930750035764890.0190259815074037
CHD2#1106310.34402283411690.0009033701102746880.00660878894276956
E2F1#186934.907389214879320.008460985347239390.0325760100523606
E2F6#187635.017155731697390.00791769806886330.0322673925396657
EGR1#195834.988179094810140.008056488137383440.0321039171498412
ELF1#199734.258097958807540.01295179875054610.046286371123333
FOS#235338.99795530889440.001372499272417130.00898360814188848
GATA1#2623313.56030814380040.0004009615963782630.00388280279686133
IRF1#365937.63716375356390.002244692747297240.0128224835002449
NFYA#4800212.28372046655370.008516011403724430.0324813276967926
NFYB#4801316.75979325353650.0002123649923296180.00246107272901831
SP1#666735.69838137814090.005403962701712170.0246822557773164
SRF#6722313.79717826216780.0003806615025800190.00375374437427576
TFAP2A#7020316.5186343730450.0002218033880766340.00248417416057218
TFAP2C#7022310.80922860986020.0007916746575753130.00616337752981797
ZBTB7A#5134137.35190930787590.002516255860282270.01403820757436



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.

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