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Difference between revisions of "Coexpression cluster:C4062"

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|full_id=C4062_argyrophil_somatostatinoma_MCF7_small_heart_neuroblastoma_cerebellum
 
|full_id=C4062_argyrophil_somatostatinoma_MCF7_small_heart_neuroblastoma_cerebellum
 
|id=C4062
 
|id=C4062
|ontology_enrichment_celltype=CL:0000066!3.94e-07!254
+
|ontology_enrichment_celltype=CL:0000066!1.68e-07!253
|ontology_enrichment_disease=DOID:0050687!2.09e-21!143;DOID:162!9.28e-17!235;DOID:14566!1.29e-15!239;DOID:305!1.38e-15!106
+
|ontology_enrichment_disease=DOID:0050687!1.72e-26!143;DOID:162!2.24e-22!235;DOID:14566!4.71e-21!239;DOID:305!2.21e-20!106;DOID:0050686!3.14e-07!137
|ontology_enrichment_uberon=UBERON:0005743!1.21e-26!86;UBERON:0000073!2.76e-25!94;UBERON:0001016!2.76e-25!94;UBERON:0001017!1.01e-24!82;UBERON:0000955!9.88e-21!69;UBERON:0006238!9.88e-21!69;UBERON:0001049!1.71e-20!57;UBERON:0005068!1.71e-20!57;UBERON:0006241!1.71e-20!57;UBERON:0007135!1.71e-20!57;UBERON:0002346!2.58e-20!90;UBERON:0003075!3.38e-19!86;UBERON:0007284!3.38e-19!86;UBERON:0002780!9.10e-18!41;UBERON:0001890!9.10e-18!41;UBERON:0006240!9.10e-18!41;UBERON:0002616!1.85e-17!59;UBERON:0007023!1.92e-17!115;UBERON:0003080!7.16e-17!42;UBERON:0000924!6.03e-16!173;UBERON:0006601!6.03e-16!173;UBERON:0004121!5.69e-15!169;UBERON:0001893!1.26e-14!34;UBERON:0002020!1.61e-14!34;UBERON:0003528!1.61e-14!34;UBERON:0001869!3.73e-14!32;UBERON:0002791!4.13e-14!33;UBERON:0003056!2.55e-13!61;UBERON:0000033!3.35e-12!123;UBERON:0000956!4.55e-12!25;UBERON:0000203!4.55e-12!25;UBERON:0002619!8.64e-12!22;UBERON:0001950!2.60e-11!20;UBERON:0000153!2.64e-11!129;UBERON:0007811!2.64e-11!129;UBERON:0000025!3.17e-09!194;UBERON:0004111!5.17e-09!241;UBERON:0000481!2.20e-08!347;UBERON:0000064!9.42e-08!219;UBERON:0000475!1.12e-07!365;UBERON:0000477!1.28e-07!286;UBERON:0000062!3.61e-07!511;UBERON:0000483!3.77e-07!309
+
|ontology_enrichment_uberon=UBERON:0001017!2.00e-25!81;UBERON:0001016!2.43e-24!89;UBERON:0000073!3.27e-23!53;UBERON:0002616!3.27e-23!53;UBERON:0000955!2.19e-22!68;UBERON:0006238!2.19e-22!68;UBERON:0001049!3.74e-22!56;UBERON:0005068!3.74e-22!56;UBERON:0006241!3.74e-22!56;UBERON:0007135!3.74e-22!56;UBERON:0002780!3.04e-20!41;UBERON:0001890!3.04e-20!41;UBERON:0003080!3.04e-20!41;UBERON:0006240!3.04e-20!41;UBERON:0002346!3.95e-19!86;UBERON:0003075!4.88e-18!82;UBERON:0007284!4.88e-18!82;UBERON:0001893!2.77e-16!34;UBERON:0003528!6.18e-16!34;UBERON:0002020!6.18e-16!34;UBERON:0011216!7.02e-16!223;UBERON:0007023!7.27e-16!114;UBERON:0001869!1.35e-15!32;UBERON:0003056!2.25e-15!61;UBERON:0002791!2.99e-15!32;UBERON:0004121!2.31e-14!171;UBERON:0000924!2.31e-14!171;UBERON:0006601!2.31e-14!171;UBERON:0000956!8.60e-14!25;UBERON:0000203!8.60e-14!25;UBERON:0010371!1.21e-13!104;UBERON:0002619!2.98e-13!22;UBERON:0001950!1.53e-12!20;UBERON:0010314!3.84e-11!132;UBERON:0000477!5.73e-08!373;UBERON:0000064!4.82e-07!218
 
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279917096206132!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325940337383473!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322862903566302!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00916111950652364!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463069703094137!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391753763782668!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294963554851662!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614636555352179!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140457106249075
 
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279917096206132!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325940337383473!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322862903566302!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00916111950652364!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463069703094137!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391753763782668!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294963554851662!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614636555352179!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140457106249075
 
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}}
 
}}

Revision as of 06:38, 19 October 2012


Full id: C4062_argyrophil_somatostatinoma_MCF7_small_heart_neuroblastoma_cerebellum



Phase1 CAGE Peaks

Hg19::chr20:62130603..62130627,-p3@EEF1A2
Hg19::chr20:62130629..62130646,-p4@EEF1A2
Hg19::chr20:62130651..62130656,-p11@EEF1A2


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
epithelial cell1.68e-07253
Uber Anatomy
Ontology termp-valuen
central nervous system2.00e-2581
nervous system2.43e-2489
regional part of nervous system3.27e-2353
regional part of brain3.27e-2353
brain2.19e-2268
future brain2.19e-2268
neural tube3.74e-2256
neural rod3.74e-2256
future spinal cord3.74e-2256
neural keel3.74e-2256
regional part of forebrain3.04e-2041
forebrain3.04e-2041
anterior neural tube3.04e-2041
future forebrain3.04e-2041
neurectoderm3.95e-1986
neural plate4.88e-1882
presumptive neural plate4.88e-1882
telencephalon2.77e-1634
brain grey matter6.18e-1634
gray matter6.18e-1634
organ system subdivision7.02e-16223
adult organism7.27e-16114
cerebral hemisphere1.35e-1532
pre-chordal neural plate2.25e-1561
regional part of telencephalon2.99e-1532
ectoderm-derived structure2.31e-14171
ectoderm2.31e-14171
presumptive ectoderm2.31e-14171
cerebral cortex8.60e-1425
pallium8.60e-1425
ecto-epithelium1.21e-13104
regional part of cerebral cortex2.98e-1322
neocortex1.53e-1220
structure with developmental contribution from neural crest3.84e-11132
anatomical cluster5.73e-08373
organ part4.82e-07218
Disease
Ontology termp-valuen
cell type cancer1.72e-26143
cancer2.24e-22235
disease of cellular proliferation4.71e-21239
carcinoma2.21e-20106
organ system cancer3.14e-07137


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#1066435.360256373075030.0064925092527670.0279917096206132
E2F1#186934.907389214879320.008460985347239390.0325940337383473
E2F6#187635.017155731697390.00791769806886330.0322862903566302
EBF1#187938.9064668465690.00141523283560980.00916111950652364
ELF1#199734.258097958807540.01295179875054610.0463069703094137
HDAC2#3066313.41562023662630.0004140761399857210.00391753763782668
MYC#460935.22228187160940.007020843755740150.0294963554851662
TCF7L2#6934310.77017656313730.0008003181298398380.00614636555352179
ZBTB7A#5134137.35190930787590.002516255860282270.0140457106249075



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.