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Coexpression cluster:C1141: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!2.22e-53!86;UBERON:0001017!2.12e-52!82;UBERON:0000073!3.00e-50!94;UBERON:0001016!3.00e-50!94;UBERON:0001049!6.94e-49!57;UBERON:0005068!6.94e-49!57;UBERON:0006241!6.94e-49!57;UBERON:0007135!6.94e-49!57;UBERON:0000955!2.24e-43!69;UBERON:0006238!2.24e-43!69;UBERON:0007023!3.50e-40!115;UBERON:0002616!5.74e-40!59;UBERON:0002780!1.10e-39!41;UBERON:0001890!1.10e-39!41;UBERON:0006240!1.10e-39!41;UBERON:0003075!1.43e-39!86;UBERON:0007284!1.43e-39!86;UBERON:0002346!4.39e-39!90;UBERON:0003080!2.44e-38!42;UBERON:0002020!5.44e-33!34;UBERON:0003528!5.44e-33!34;UBERON:0001893!9.55e-33!34;UBERON:0002791!7.75e-32!33;UBERON:0001869!1.11e-30!32;UBERON:0003056!5.38e-30!61;UBERON:0000153!5.54e-26!129;UBERON:0007811!5.54e-26!129;UBERON:0000924!1.83e-25!173;UBERON:0006601!1.83e-25!173;UBERON:0004121!2.86e-25!169;UBERON:0000033!1.03e-24!123;UBERON:0000956!5.46e-24!25;UBERON:0000203!5.46e-24!25;UBERON:0002619!6.18e-22!22;UBERON:0001950!6.79e-20!20;UBERON:0003076!1.96e-11!15;UBERON:0003057!1.96e-11!15;UBERON:0000025!8.16e-11!194;UBERON:0002308!2.14e-10!9;UBERON:0000125!2.14e-10!9;UBERON:0002420!4.54e-10!9;UBERON:0007245!4.54e-10!9;UBERON:0010009!4.54e-10!9;UBERON:0010011!4.54e-10!9;UBERON:0000454!4.54e-10!9;UBERON:0004732!3.59e-09!13;UBERON:0000062!7.62e-09!511;UBERON:0001871!8.83e-09!7;UBERON:0004733!1.62e-08!12;UBERON:0002028!1.62e-08!12;UBERON:0007277!1.62e-08!12;UBERON:0001894!2.93e-08!7;UBERON:0006222!2.93e-08!7;UBERON:0009663!3.23e-08!7;UBERON:0000064!3.51e-08!219;UBERON:0002298!1.16e-07!8;UBERON:0004111!1.53e-07!241;UBERON:0000481!2.81e-07!347;UBERON:0000483!5.58e-07!309;UBERON:0000475!5.86e-07!365;UBERON:0000200!8.39e-07!6
|ontology_enrichment_uberon=UBERON:0005743!2.22e-53!86;UBERON:0001017!2.12e-52!82;UBERON:0000073!3.00e-50!94;UBERON:0001016!3.00e-50!94;UBERON:0001049!6.94e-49!57;UBERON:0005068!6.94e-49!57;UBERON:0006241!6.94e-49!57;UBERON:0007135!6.94e-49!57;UBERON:0000955!2.24e-43!69;UBERON:0006238!2.24e-43!69;UBERON:0007023!3.50e-40!115;UBERON:0002616!5.74e-40!59;UBERON:0002780!1.10e-39!41;UBERON:0001890!1.10e-39!41;UBERON:0006240!1.10e-39!41;UBERON:0003075!1.43e-39!86;UBERON:0007284!1.43e-39!86;UBERON:0002346!4.39e-39!90;UBERON:0003080!2.44e-38!42;UBERON:0002020!5.44e-33!34;UBERON:0003528!5.44e-33!34;UBERON:0001893!9.55e-33!34;UBERON:0002791!7.75e-32!33;UBERON:0001869!1.11e-30!32;UBERON:0003056!5.38e-30!61;UBERON:0000153!5.54e-26!129;UBERON:0007811!5.54e-26!129;UBERON:0000924!1.83e-25!173;UBERON:0006601!1.83e-25!173;UBERON:0004121!2.86e-25!169;UBERON:0000033!1.03e-24!123;UBERON:0000956!5.46e-24!25;UBERON:0000203!5.46e-24!25;UBERON:0002619!6.18e-22!22;UBERON:0001950!6.79e-20!20;UBERON:0003076!1.96e-11!15;UBERON:0003057!1.96e-11!15;UBERON:0000025!8.16e-11!194;UBERON:0002308!2.14e-10!9;UBERON:0000125!2.14e-10!9;UBERON:0002420!4.54e-10!9;UBERON:0007245!4.54e-10!9;UBERON:0010009!4.54e-10!9;UBERON:0010011!4.54e-10!9;UBERON:0000454!4.54e-10!9;UBERON:0004732!3.59e-09!13;UBERON:0000062!7.62e-09!511;UBERON:0001871!8.83e-09!7;UBERON:0004733!1.62e-08!12;UBERON:0002028!1.62e-08!12;UBERON:0007277!1.62e-08!12;UBERON:0001894!2.93e-08!7;UBERON:0006222!2.93e-08!7;UBERON:0009663!3.23e-08!7;UBERON:0000064!3.51e-08!219;UBERON:0002298!1.16e-07!8;UBERON:0004111!1.53e-07!241;UBERON:0000481!2.81e-07!347;UBERON:0000483!5.58e-07!309;UBERON:0000475!5.86e-07!365;UBERON:0000200!8.39e-07!6
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}}
}}

Revision as of 16:56, 8 August 2012


Full id: C1141_argyrophil_pituitary_nonsmall_small_medulla_locus_temporal



Phase1 CAGE Peaks

Hg19::chr11:45918158..45918189,+p8@MAPK8IP1
Hg19::chr15:75488008..75488019,+p@chr15:75488008..75488019
+
Hg19::chr16:8814563..8814603,+p6@ABAT
Hg19::chr1:206223941..206223944,+p1@AVPR1B
Hg19::chr1:240286448..240286474,+p@chr1:240286448..240286474
+
Hg19::chr4:8012461..8012482,-p6@ABLIM2
Hg19::chrX:118608746..118608769,+p@chrX:118608746..118608769
+


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


GO IDGO nameFDR corrected p-value
GO:0019899enzyme binding0.000532460199117048
GO:0019901protein kinase binding0.00275226657247145
GO:0019900kinase binding0.00275226657247145
GO:00038674-aminobutyrate transaminase activity0.00275226657247145
GO:0047298(S)-3-amino-2-methylpropionate transaminase activity0.00275226657247145
GO:0032145succinate-semialdehyde dehydrogenase binding0.00275226657247145
GO:00321444-aminobutyrate transaminase complex0.00275226657247145
GO:0042538hyperosmotic salinity response0.00275226657247145
GO:0009448gamma-aminobutyric acid metabolic process0.00293562138164337
GO:0009651response to salt stress0.00293562138164337
GO:0048148behavioral response to cocaine0.00293562138164337
GO:0019626short-chain fatty acid catabolic process0.00293562138164337
GO:0046359butyrate catabolic process0.00293562138164337
GO:0019605butyrate metabolic process0.00293562138164337
GO:0009450gamma-aminobutyric acid catabolic process0.00293562138164337
GO:0001992regulation of systemic arterial blood pressure by vasopressin0.00330242822745582
GO:0006972hyperosmotic response0.00330242822745582
GO:0005078MAP-kinase scaffold activity0.00330242822745582
GO:0042220response to cocaine0.00330242822745582
GO:0014073response to tropane0.00330242822745582
GO:0046459short-chain fatty acid metabolic process0.00419337448417358
GO:0009062fatty acid catabolic process0.00500323725885042
GO:0006970response to osmotic stress0.00647334823424654
GO:0042135neurotransmitter catabolic process0.00647334823424654
GO:0043279response to alkaloid0.00647334823424654
GO:0050886endocrine process0.00647334823424654
GO:0001990regulation of systemic arterial blood pressure by hormone0.00647334823424654
GO:0019894kinesin binding0.00647334823424654
GO:0017046peptide hormone binding0.00647334823424654
GO:0005000vasopressin receptor activity0.00647334823424654
GO:0046395carboxylic acid catabolic process0.00647334823424654
GO:0016054organic acid catabolic process0.00647334823424654
GO:0005080protein kinase C binding0.00647334823424654
GO:0001603vasopressin-like receptor activity0.00647334823424654
GO:0014070response to organic cyclic substance0.00691692952418288
GO:0003044regulation of systemic arterial blood pressure mediated by a chemical signal0.0073358134288381
GO:0042219amino acid derivative catabolic process0.00832640416780392
GO:0008092cytoskeletal protein binding0.00880142132979071
GO:0007202phospholipase C activation0.00880142132979071
GO:0003073regulation of systemic arterial blood pressure0.00880142132979071
GO:0030159receptor signaling complex scaffold activity0.00965924344639748
GO:0046328regulation of JNK cascade0.00995266979920516
GO:0005737cytoplasm0.00999984862400368
GO:0032947protein complex scaffold0.00999984862400368
GO:0019439aromatic compound catabolic process0.0102660578907856
GO:0042562hormone binding0.0124313000723987
GO:0030534adult behavior0.0126342003787232
GO:0042133neurotransmitter metabolic process0.0146586743863171
GO:0004860protein kinase inhibitor activity0.0179430566270281
GO:0005515protein binding0.0180997788971695
GO:0019210kinase inhibitor activity0.0180997788971695
GO:0008483transaminase activity0.0194389104962489
GO:0044242cellular lipid catabolic process0.0198996041632521
GO:0008217regulation of blood pressure0.0223724594128333
GO:0016769transferase activity, transferring nitrogenous groups0.0243116360946388
GO:0010033response to organic substance0.0243116360946388
GO:0007254JNK cascade0.0250375296718024
GO:0031098stress-activated protein kinase signaling pathway0.025609662230631
GO:0051480cytosolic calcium ion homeostasis0.025609662230631
GO:0007204elevation of cytosolic calcium ion concentration0.025609662230631
GO:0051345positive regulation of hydrolase activity0.0273417127902622
GO:0001505regulation of neurotransmitter levels0.0276061920576986
GO:0043229intracellular organelle0.0294816676800128
GO:0043226organelle0.0294816676800128
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.029694844998741
GO:0006575amino acid derivative metabolic process0.0299069380436163
GO:0003008system process0.0323096681837383
GO:0019887protein kinase regulator activity0.0338427757439054
GO:0006874cellular calcium ion homeostasis0.0360979764961657
GO:0055074calcium ion homeostasis0.0360979764961657
GO:0030170pyridoxal phosphate binding0.0360979764961657
GO:0019207kinase regulator activity0.0364010246706387
GO:0006875cellular metal ion homeostasis0.0364010246706387
GO:0055065metal ion homeostasis0.0364010246706387
GO:0048015phosphoinositide-mediated signaling0.0376576776302515
GO:0007154cell communication0.0378359583518643
GO:0016042lipid catabolic process0.0409821848022357
GO:0001653peptide receptor activity0.0409821848022357
GO:0008528peptide receptor activity, G-protein coupled0.0409821848022357
GO:0000165MAPKKK cascade0.0410131733915982
GO:0042803protein homodimerization activity0.0416457691005139
GO:0007242intracellular signaling cascade0.0416457691005139
GO:0008015blood circulation0.0416457691005139
GO:0003013circulatory system process0.0416457691005139
GO:0009628response to abiotic stimulus0.04243256151255
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0439236533691728
GO:0044424intracellular part0.0439236533691728
GO:0031980mitochondrial lumen0.0439236533691728
GO:0055066di-, tri-valent inorganic cation homeostasis0.0439236533691728
GO:0006725aromatic compound metabolic process0.0439236533691728
GO:0005759mitochondrial matrix0.0439236533691728
GO:0006631fatty acid metabolic process0.0453076123791525
GO:0005768endosome0.0453076123791525
GO:0030003cellular cation homeostasis0.0464370468193041
GO:0055080cation homeostasis0.0466312757290864
GO:0042277peptide binding0.0472716745516595



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><br>


Cell Type
Ontology termp-valuen
neural cell3.83e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system2.12e-5282
regional part of nervous system3.00e-5094
nervous system3.00e-5094
neural tube6.94e-4957
neural rod6.94e-4957
future spinal cord6.94e-4957
neural keel6.94e-4957
brain2.24e-4369
future brain2.24e-4369
adult organism3.50e-40115
regional part of brain5.74e-4059
regional part of forebrain1.10e-3941
forebrain1.10e-3941
future forebrain1.10e-3941
neural plate1.43e-3986
presumptive neural plate1.43e-3986
neurectoderm4.39e-3990
anterior neural tube2.44e-3842
gray matter5.44e-3334
brain grey matter5.44e-3334
telencephalon9.55e-3334
regional part of telencephalon7.75e-3233
cerebral hemisphere1.11e-3032
pre-chordal neural plate5.38e-3061
anterior region of body5.54e-26129
craniocervical region5.54e-26129
ectoderm1.83e-25173
presumptive ectoderm1.83e-25173
ectoderm-derived structure2.86e-25169
head1.03e-24123
cerebral cortex5.46e-2425
pallium5.46e-2425
regional part of cerebral cortex6.18e-2222
neocortex6.79e-2020
posterior neural tube1.96e-1115
chordal neural plate1.96e-1115
tube8.16e-11194
nucleus of brain2.14e-109
neural nucleus2.14e-109
basal ganglion4.54e-109
nuclear complex of neuraxis4.54e-109
aggregate regional part of brain4.54e-109
collection of basal ganglia4.54e-109
cerebral subcortex4.54e-109
segmental subdivision of nervous system3.59e-0913
organ7.62e-09511
temporal lobe8.83e-097
segmental subdivision of hindbrain1.62e-0812
hindbrain1.62e-0812
presumptive hindbrain1.62e-0812
diencephalon2.93e-087
future diencephalon2.93e-087
telencephalic nucleus3.23e-087
organ part3.51e-08219
brainstem1.16e-078
anatomical conduit1.53e-07241
multi-tissue structure2.81e-07347
epithelium5.58e-07309
organism subdivision5.86e-07365
gyrus8.39e-076


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


No analysis results for this cluster

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.