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Coexpression cluster:C1038: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!6.48e-45!115;UBERON:0001049!6.52e-34!57;UBERON:0005068!6.52e-34!57;UBERON:0006241!6.52e-34!57;UBERON:0007135!6.52e-34!57;UBERON:0005743!1.83e-33!86;UBERON:0001017!3.06e-33!82;UBERON:0000073!2.79e-31!94;UBERON:0001016!2.79e-31!94;UBERON:0002616!2.48e-30!59;UBERON:0003075!2.35e-29!86;UBERON:0007284!2.35e-29!86;UBERON:0002346!1.27e-28!90;UBERON:0000955!1.58e-27!69;UBERON:0006238!1.58e-27!69;UBERON:0004121!1.34e-25!169;UBERON:0000924!1.95e-25!173;UBERON:0006601!1.95e-25!173;UBERON:0003080!3.01e-25!42;UBERON:0002780!4.55e-25!41;UBERON:0001890!4.55e-25!41;UBERON:0006240!4.55e-25!41;UBERON:0000033!2.96e-22!123;UBERON:0000153!4.17e-22!129;UBERON:0007811!4.17e-22!129;UBERON:0001893!1.80e-21!34;UBERON:0002020!1.91e-21!34;UBERON:0003528!1.91e-21!34;UBERON:0003056!3.68e-21!61;UBERON:0002791!7.49e-21!33;UBERON:0001869!3.27e-20!32;UBERON:0000956!6.13e-16!25;UBERON:0000203!6.13e-16!25;UBERON:0002619!1.98e-14!22;UBERON:0000475!1.96e-13!365;UBERON:0001950!3.46e-13!20;UBERON:0000481!1.35e-11!347;UBERON:0000477!8.80e-11!286;UBERON:0004111!1.04e-10!241;UBERON:0003076!1.09e-09!15;UBERON:0003057!1.09e-09!15;UBERON:0000025!1.42e-09!194;UBERON:0000064!1.70e-09!219;UBERON:0000483!5.54e-09!309;UBERON:0000119!9.11e-09!312;UBERON:0004732!2.34e-08!13;UBERON:0004733!7.50e-08!12;UBERON:0002028!7.50e-08!12;UBERON:0007277!7.50e-08!12;UBERON:0000062!1.95e-07!511;UBERON:0002420!5.54e-07!9;UBERON:0007245!5.54e-07!9;UBERON:0010009!5.54e-07!9;UBERON:0010011!5.54e-07!9;UBERON:0000454!5.54e-07!9;UBERON:0000468!5.59e-07!659;UBERON:0002308!5.73e-07!9;UBERON:0000125!5.73e-07!9
|ontology_enrichment_uberon=UBERON:0007023!6.48e-45!115;UBERON:0001049!6.52e-34!57;UBERON:0005068!6.52e-34!57;UBERON:0006241!6.52e-34!57;UBERON:0007135!6.52e-34!57;UBERON:0005743!1.83e-33!86;UBERON:0001017!3.06e-33!82;UBERON:0000073!2.79e-31!94;UBERON:0001016!2.79e-31!94;UBERON:0002616!2.48e-30!59;UBERON:0003075!2.35e-29!86;UBERON:0007284!2.35e-29!86;UBERON:0002346!1.27e-28!90;UBERON:0000955!1.58e-27!69;UBERON:0006238!1.58e-27!69;UBERON:0004121!1.34e-25!169;UBERON:0000924!1.95e-25!173;UBERON:0006601!1.95e-25!173;UBERON:0003080!3.01e-25!42;UBERON:0002780!4.55e-25!41;UBERON:0001890!4.55e-25!41;UBERON:0006240!4.55e-25!41;UBERON:0000033!2.96e-22!123;UBERON:0000153!4.17e-22!129;UBERON:0007811!4.17e-22!129;UBERON:0001893!1.80e-21!34;UBERON:0002020!1.91e-21!34;UBERON:0003528!1.91e-21!34;UBERON:0003056!3.68e-21!61;UBERON:0002791!7.49e-21!33;UBERON:0001869!3.27e-20!32;UBERON:0000956!6.13e-16!25;UBERON:0000203!6.13e-16!25;UBERON:0002619!1.98e-14!22;UBERON:0000475!1.96e-13!365;UBERON:0001950!3.46e-13!20;UBERON:0000481!1.35e-11!347;UBERON:0000477!8.80e-11!286;UBERON:0004111!1.04e-10!241;UBERON:0003076!1.09e-09!15;UBERON:0003057!1.09e-09!15;UBERON:0000025!1.42e-09!194;UBERON:0000064!1.70e-09!219;UBERON:0000483!5.54e-09!309;UBERON:0000119!9.11e-09!312;UBERON:0004732!2.34e-08!13;UBERON:0004733!7.50e-08!12;UBERON:0002028!7.50e-08!12;UBERON:0007277!7.50e-08!12;UBERON:0000062!1.95e-07!511;UBERON:0002420!5.54e-07!9;UBERON:0007245!5.54e-07!9;UBERON:0010009!5.54e-07!9;UBERON:0010011!5.54e-07!9;UBERON:0000454!5.54e-07!9;UBERON:0000468!5.59e-07!659;UBERON:0002308!5.73e-07!9;UBERON:0000125!5.73e-07!9
|pathway_enrichment=6.95890409625456e-06;0.00220249314646457;2;44;Valine, leucine and isoleucine degradation (KEGG):00280!3.64966676839917e-06;0.00220249314646457;2;32;Propanoate metabolism (KEGG):00640
|pathway_enrichment=6.95890409625456e-06;0.00220249314646457;2;44;Valine, leucine and isoleucine degradation (KEGG):00280!3.64966676839917e-06;0.00220249314646457;2;32;Propanoate metabolism (KEGG):00640
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}}
}}

Revision as of 11:56, 5 September 2012


Full id: C1038_Hepatocyte_liver_hippocampus_amygdala_caudate_corpus_thalamus



Phase1 CAGE Peaks

Hg19::chr14:74551096..74551171,-p1@ALDH6A1
Hg19::chr16:8768441..8768452,+p5@ABAT
Hg19::chr8:27468842..27468878,-p12@CLU
Hg19::chr8:27468880..27468910,-p11@CLU
Hg19::chr8:27468913..27468922,-p35@CLU
Hg19::chr8:27468927..27468936,-p37@CLU
Hg19::chr8:27468945..27468948,-p48@CLU
Hg19::chr8:27468954..27468973,-p21@CLU


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


p.valueFDRnGenesnPathwayName
6.95890409625456e-060.00220249314646457244Valine, leucine and isoleucine degradation (KEGG):00280
3.64966676839917e-060.00220249314646457232Propanoate metabolism (KEGG):00640



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:0006725aromatic compound metabolic process0.00209725369783426
GO:00038674-aminobutyrate transaminase activity0.00209725369783426
GO:0019859thymine metabolic process0.00209725369783426
GO:0018478malonate-semialdehyde dehydrogenase (acetylating) activity0.00209725369783426
GO:0047298(S)-3-amino-2-methylpropionate transaminase activity0.00209725369783426
GO:0032145succinate-semialdehyde dehydrogenase binding0.00209725369783426
GO:0004491methylmalonate-semialdehyde dehydrogenase (acylating) activity0.00209725369783426
GO:00321444-aminobutyrate transaminase complex0.00209725369783426
GO:0009448gamma-aminobutyric acid metabolic process0.00209725369783426
GO:0048148behavioral response to cocaine0.00209725369783426
GO:0019626short-chain fatty acid catabolic process0.00209725369783426
GO:0046359butyrate catabolic process0.00209725369783426
GO:0006573valine metabolic process0.00209725369783426
GO:0019605butyrate metabolic process0.00209725369783426
GO:0016235aggresome0.00209725369783426
GO:0009450gamma-aminobutyric acid catabolic process0.00209725369783426
GO:0042220response to cocaine0.00279625594751804
GO:0014073response to tropane0.00279625594751804
GO:0046459short-chain fatty acid metabolic process0.00353200879941799
GO:0009062fatty acid catabolic process0.0041941369797639
GO:0048037cofactor binding0.00424254131842541
GO:0016234inclusion body0.00437636192623535
GO:0031018endocrine pancreas development0.00437636192623535
GO:0042135neurotransmitter catabolic process0.00536802122965575
GO:0043279response to alkaloid0.00536802122965575
GO:0006519amino acid and derivative metabolic process0.0056332784920928
GO:0046395carboxylic acid catabolic process0.00563617767666475
GO:0031016pancreas development0.00563617767666475
GO:0016054organic acid catabolic process0.00563617767666475
GO:0042221response to chemical stimulus0.00563617767666475
GO:0014070response to organic cyclic substance0.00595191720609126
GO:0009308amine metabolic process0.00615585991956573
GO:0006206pyrimidine base metabolic process0.00657937560058684
GO:0006807nitrogen compound metabolic process0.00657937560058684
GO:0042219amino acid derivative catabolic process0.00670884138064908
GO:0009081branched chain family amino acid metabolic process0.00745382928836276
GO:0019752carboxylic acid metabolic process0.00813738920926449
GO:0006082organic acid metabolic process0.00813738920926449
GO:0000062acyl-CoA binding0.00859955944077925
GO:0019439aromatic compound catabolic process0.0088035397728746
GO:0009112nucleobase metabolic process0.00940624816327905
GO:0006629lipid metabolic process0.0103180539925961
GO:0030534adult behavior0.0104316746465184
GO:0044444cytoplasmic part0.0104316746465184
GO:0006958complement activation, classical pathway0.0104316746465184
GO:0005739mitochondrion0.0105162913588557
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0107005558179499
GO:0005504fatty acid binding0.0108265630239047
GO:0042133neurotransmitter metabolic process0.0109474069369195
GO:0035270endocrine system development0.0110633973551524
GO:0006956complement activation0.0125698213712117
GO:0002541activation of plasma proteins during acute inflammatory response0.0125698213712117
GO:0008483transaminase activity0.0145432100741649
GO:0045597positive regulation of cell differentiation0.0145837638527713
GO:0044242cellular lipid catabolic process0.014622825012576
GO:0016620oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor0.014959226279668
GO:0016064immunoglobulin mediated immune response0.014990277895566
GO:0019724B cell mediated immunity0.0150202417598716
GO:0016769transferase activity, transferring nitrogenous groups0.0173066933148615
GO:0010033response to organic substance0.0173066933148615
GO:0048471perinuclear region of cytoplasm0.0175710701776496
GO:0051094positive regulation of developmental process0.0182656147218351
GO:0006220pyrimidine nucleotide metabolic process0.0182656147218351
GO:0002253activation of immune response0.0182656147218351
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.0182656147218351
GO:0002449lymphocyte mediated immunity0.0182656147218351
GO:0006959humoral immune response0.0183675305377231
GO:0002250adaptive immune response0.0183675305377231
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0183675305377231
GO:0002443leukocyte mediated immunity0.0183675305377231
GO:0001505regulation of neurotransmitter levels0.0183675305377231
GO:0002526acute inflammatory response0.0183675305377231
GO:0050778positive regulation of immune response0.0194506153245901
GO:0002684positive regulation of immune system process0.0194506153245901
GO:0006575amino acid derivative metabolic process0.0200815244420623
GO:0050776regulation of immune response0.0215737452949274
GO:0002682regulation of immune system process0.0217268489507706
GO:0051240positive regulation of multicellular organismal process0.0225173967991115
GO:0002252immune effector process0.0232876191353746
GO:0045087innate immune response0.023829951962537
GO:0030170pyridoxal phosphate binding0.0238719907821851
GO:0048667neuron morphogenesis during differentiation0.0238719907821851
GO:0006979response to oxidative stress0.0238719907821851
GO:0048812neurite morphogenesis0.0238719907821851
GO:0005737cytoplasm0.0238719907821851
GO:0000904cellular morphogenesis during differentiation0.0244921440189288
GO:0046483heterocycle metabolic process0.0249762716353216
GO:0031175neurite development0.0256383812428713
GO:0045595regulation of cell differentiation0.0270331574805088
GO:0016042lipid catabolic process0.0271024798592471
GO:0048666neuron development0.0282667311209228
GO:0042803protein homodimerization activity0.0286823217678161
GO:0006916anti-apoptosis0.030518090645957
GO:0031980mitochondrial lumen0.032147883579936
GO:0005759mitochondrial matrix0.032147883579936
GO:0006631fatty acid metabolic process0.0331959097229849
GO:0032990cell part morphogenesis0.0343677338044235
GO:0048858cell projection morphogenesis0.0343677338044235
GO:0030030cell projection organization and biogenesis0.0343677338044235
GO:0030182neuron differentiation0.0350185658761542
GO:0043066negative regulation of apoptosis0.0374598251978158
GO:0043069negative regulation of programmed cell death0.0375794559595029
GO:0008284positive regulation of cell proliferation0.0376966780617515
GO:0050793regulation of developmental process0.0378115609926719
GO:0048699generation of neurons0.0383968082218322
GO:0019842vitamin binding0.0385026686984877
GO:0022008neurogenesis0.0407690182779484
GO:0051239regulation of multicellular organismal process0.0426851176233368
GO:0032787monocarboxylic acid metabolic process0.0432231044820223
GO:0050662coenzyme binding0.0432231044820223
GO:0007268synaptic transmission0.0432231044820223
GO:0006954inflammatory response0.0432231044820223
GO:0007610behavior0.0432784217108178
GO:0019899enzyme binding0.0444893924724475
GO:0019226transmission of nerve impulse0.0476822767761628
GO:0009117nucleotide metabolic process0.048689302116024



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 organism6.48e-45115
neural tube6.52e-3457
neural rod6.52e-3457
future spinal cord6.52e-3457
neural keel6.52e-3457
central nervous system3.06e-3382
regional part of nervous system2.79e-3194
nervous system2.79e-3194
regional part of brain2.48e-3059
neural plate2.35e-2986
presumptive neural plate2.35e-2986
neurectoderm1.27e-2890
brain1.58e-2769
future brain1.58e-2769
ectoderm-derived structure1.34e-25169
ectoderm1.95e-25173
presumptive ectoderm1.95e-25173
anterior neural tube3.01e-2542
regional part of forebrain4.55e-2541
forebrain4.55e-2541
future forebrain4.55e-2541
head2.96e-22123
anterior region of body4.17e-22129
craniocervical region4.17e-22129
telencephalon1.80e-2134
gray matter1.91e-2134
brain grey matter1.91e-2134
pre-chordal neural plate3.68e-2161
regional part of telencephalon7.49e-2133
cerebral hemisphere3.27e-2032
cerebral cortex6.13e-1625
pallium6.13e-1625
regional part of cerebral cortex1.98e-1422
organism subdivision1.96e-13365
neocortex3.46e-1320
multi-tissue structure1.35e-11347
anatomical cluster8.80e-11286
anatomical conduit1.04e-10241
posterior neural tube1.09e-0915
chordal neural plate1.09e-0915
tube1.42e-09194
organ part1.70e-09219
epithelium5.54e-09309
cell layer9.11e-09312
segmental subdivision of nervous system2.34e-0813
segmental subdivision of hindbrain7.50e-0812
hindbrain7.50e-0812
presumptive hindbrain7.50e-0812
organ1.95e-07511
basal ganglion5.54e-079
nuclear complex of neuraxis5.54e-079
aggregate regional part of brain5.54e-079
collection of basal ganglia5.54e-079
cerebral subcortex5.54e-079
multi-cellular organism5.59e-07659
nucleus of brain5.73e-079
neural nucleus5.73e-079


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
CEBPB#105165.978360719368618.69217560109361e-050.0013016950496166
EP300#203386.77394172622322.25366016107097e-071.18993940122392e-05
STAT3#677467.889598747865681.7423325560997e-050.000398178270955136



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.