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{{Coexpression_clusters
{
|full_id=C1038_Hepatocyte_liver_hippocampus_amygdala_caudate_corpus_thalamus
|gostat_on_coexpression_clusters

Latest revision as of 11:36, 17 September 2013


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
neural tube3.55e-6956
neural rod3.55e-6956
future spinal cord3.55e-6956
neural keel3.55e-6956
adult organism1.14e-65114
regional part of nervous system2.16e-6453
regional part of brain2.16e-6453
central nervous system2.10e-6081
nervous system2.58e-5689
neural plate1.76e-5382
presumptive neural plate1.76e-5382
brain2.38e-5268
future brain2.38e-5268
neurectoderm4.20e-5086
regional part of forebrain1.02e-4941
forebrain1.02e-4941
anterior neural tube1.02e-4941
future forebrain1.02e-4941
brain grey matter1.02e-4534
gray matter1.02e-4534
telencephalon1.10e-4534
cerebral hemisphere9.97e-4332
regional part of telencephalon1.31e-4232
ecto-epithelium9.02e-40104
pre-chordal neural plate8.15e-3761
cerebral cortex3.46e-3225
pallium3.46e-3225
structure with developmental contribution from neural crest4.18e-32132
organ system subdivision2.02e-31223
ectoderm-derived structure4.72e-29171
ectoderm4.72e-29171
presumptive ectoderm4.72e-29171
regional part of cerebral cortex1.87e-2822
neocortex1.90e-2520
tube2.18e-21192
posterior neural tube9.69e-2015
chordal neural plate9.69e-2015
anatomical cluster4.37e-19373
anatomical conduit5.36e-17240
segmental subdivision of nervous system1.34e-1613
segmental subdivision of hindbrain2.72e-1512
hindbrain2.72e-1512
presumptive hindbrain2.72e-1512
neural nucleus7.00e-159
nucleus of brain7.00e-159
basal ganglion8.10e-159
nuclear complex of neuraxis8.10e-159
aggregate regional part of brain8.10e-159
collection of basal ganglia8.10e-159
cerebral subcortex8.10e-159
multi-tissue structure6.00e-13342
telencephalic nucleus7.24e-127
epithelium8.58e-12306
organ part1.18e-11218
cell layer1.76e-11309
regional part of metencephalon8.26e-119
metencephalon8.26e-119
future metencephalon8.26e-119
brainstem1.14e-106
gyrus1.74e-106
organ3.43e-10503
limbic system3.69e-095
germ layer1.18e-08560
germ layer / neural crest1.18e-08560
embryonic tissue1.18e-08560
presumptive structure1.18e-08560
germ layer / neural crest derived structure1.18e-08560
epiblast (generic)1.18e-08560
occipital lobe1.26e-085
temporal lobe1.49e-086
embryonic structure2.14e-08564
embryo5.43e-08592
corpus striatum8.25e-084
striatum8.25e-084
ventral part of telencephalon8.25e-084
future corpus striatum8.25e-084
developing anatomical structure8.42e-08581
anatomical system2.59e-07624
anatomical group2.96e-07625
multi-cellular organism3.26e-07656
regional part of diencephalon5.31e-074


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)
MA0003.10.393486
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.275152
MA0017.13.35603
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.11.3714
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.11.12793
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.0912556
MA0058.11.69448
MA0059.10.948176
MA0060.13.1469
MA0061.12.9227
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.19.73652
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.11.87644
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.12.65557
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.12.18672
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.11.07975
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.13.31023
MA0106.10.59853
MA0107.11.23931
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.14.41429
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.913661
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.15.63072
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.14.28036
MA0145.10.0613434
MA0146.10.418694
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.23.26158
MA0039.23.00692
MA0138.20.653421
MA0002.20.179788
MA0137.24.22944
MA0104.20.189646
MA0047.20.586412
MA0112.24.90171
MA0065.23.62396
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.764865
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.11.96124
MA0160.10.495355
MA0161.10
MA0162.10.378102
MA0163.10.0517199
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.21.97275
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
MA0442.10



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.

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