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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 10:05, 17 September 2013


Full id: C10_occipital_temporal_parietal_brain_duodenum_Neurons_Neural



Phase1 CAGE Peaks


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
1.50639613609536e-060.000476774377074182987ErbB signaling pathway (KEGG):04012
4.03493974149437e-050.003638559504893319130Axon guidance (KEGG):04360
0.0001408860821190450.00990898777570619790Gap junction (KEGG):04540
0.0002489484145450590.0143258496733657670Long-term potentiation (KEGG):04720
4.51163032377388e-060.0009519539983162910126Glutamatergic synapse (KEGG):04724
0.0005403507190190340.0285035004282547112Wnt Signaling Pathway NetPath (Wikipathways):WP363
0.0007956904001755160.0387440017931617315GPCRs, Class C Metabotropic glutamate, pheromone (Wikipathways):WP501
4.59849542482566e-050.00363855950489331532Hypothetical Network for Drug Addiction (Wikipathways):WP666
8.01823943464713e-060.0010151091124263312197Synaptic Transmission (Reactome):REACT_13685
5.4385689802965e-143.44261416452769e-1124265Axon guidance (Reactome):REACT_18266
2.33856132254937e-050.00246718219528959528{DLG4,28} (Static Module):NA
0.0002198635179773240.0139173606879646310{PAK2,10} (Static Module):NA
6.8388258594864e-060.0010151091124263310132{RAC1,133} (Static Module):NA



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:0007399nervous system development0
GO:0048731system development3.42916750319792e-38
GO:0048856anatomical structure development3.66233684922925e-34
GO:0007275multicellular organismal development1.51604183866946e-30
GO:0032501multicellular organismal process3.53092113255232e-25
GO:0032502developmental process6.77432320723079e-25
GO:0030182neuron differentiation3.5557282734419e-16
GO:0005856cytoskeleton9.02523401205732e-16
GO:0048699generation of neurons6.64483131866011e-15
GO:0022008neurogenesis3.450544579738e-14
GO:0005515protein binding3.52779871747566e-14
GO:0044464cell part4.66400648694327e-13
GO:0048869cellular developmental process4.82965222239229e-13
GO:0030154cell differentiation4.82965222239229e-13
GO:0016020membrane6.70703301551283e-13
GO:0005886plasma membrane2.29518497285206e-12
GO:0007267cell-cell signaling2.90829318129329e-12
GO:0031175neurite development6.8168318272438e-12
GO:0016043cellular component organization and biogenesis1.80595350629252e-11
GO:0044425membrane part2.19105363050995e-11
GO:0048666neuron development4.64857080063647e-11
GO:0007010cytoskeleton organization and biogenesis5.27810979863882e-11
GO:0009653anatomical structure morphogenesis7.98231720510016e-11
GO:0008092cytoskeletal protein binding9.0025853354009e-11
GO:0000902cell morphogenesis9.10035609909797e-11
GO:0032989cellular structure morphogenesis9.10035609909797e-11
GO:0007154cell communication8.49180039197281e-10
GO:0007268synaptic transmission9.2065834010474e-10
GO:0007409axonogenesis1.50834744457238e-09
GO:0048858cell projection morphogenesis2.25711452284648e-09
GO:0032990cell part morphogenesis2.25711452284648e-09
GO:0030030cell projection organization and biogenesis2.25711452284648e-09
GO:0048667neuron morphogenesis during differentiation2.47960641877007e-09
GO:0048812neurite morphogenesis2.47960641877007e-09
GO:0000904cellular morphogenesis during differentiation4.47760845004081e-09
GO:0019226transmission of nerve impulse6.53387227446778e-09
GO:0031224intrinsic to membrane8.9114154883612e-09
GO:0044459plasma membrane part1.24743624720511e-08
GO:0030054cell junction1.2796607339596e-08
GO:0007417central nervous system development1.45911773509788e-08
GO:0016021integral to membrane1.45911773509788e-08
GO:0005737cytoplasm6.48839158082037e-08
GO:0007420brain development1.49530239446313e-07
GO:0007165signal transduction2.397293477489e-07
GO:0048468cell development3.91241223927337e-07
GO:0050789regulation of biological process8.58264685933664e-07
GO:0031114regulation of microtubule depolymerization8.71715035020438e-07
GO:0007026negative regulation of microtubule depolymerization8.71715035020438e-07
GO:0044424intracellular part9.8327962522705e-07
GO:0030295protein kinase activator activity1.08054308042338e-06
GO:0007019microtubule depolymerization1.08054308042338e-06
GO:0031111negative regulation of microtubule polymerization or depolymerization1.08054308042338e-06
GO:0043005neuron projection1.16449174378467e-06
GO:0065007biological regulation1.17555022143405e-06
GO:0051261protein depolymerization3.9839689816965e-06
GO:0007017microtubule-based process4.34238409436252e-06
GO:0031110regulation of microtubule polymerization or depolymerization4.43509360761182e-06
GO:0044456synapse part5.41727200793187e-06
GO:0031109microtubule polymerization or depolymerization7.99276122061449e-06
GO:0051129negative regulation of cellular component organization and biogenesis8.72132651833816e-06
GO:0050794regulation of cellular process8.72620938362211e-06
GO:0019209kinase activator activity8.94222759115674e-06
GO:0030426growth cone8.94222759115674e-06
GO:0005874microtubule1.14198782680398e-05
GO:0005622intracellular1.14198782680398e-05
GO:0030427site of polarized growth1.15000456113826e-05
GO:0007411axon guidance1.31339501353869e-05
GO:0007242intracellular signaling cascade1.39609022316097e-05
GO:0045211postsynaptic membrane1.88628029485488e-05
GO:0042995cell projection1.88628029485488e-05
GO:0015630microtubule cytoskeleton2.07344557160584e-05
GO:0004157dihydropyrimidinase activity5.16732416657154e-05
GO:0043228non-membrane-bound organelle6.08075555053569e-05
GO:0043232intracellular non-membrane-bound organelle6.08075555053569e-05
GO:0048523negative regulation of cellular process6.70586829170916e-05
GO:0005794Golgi apparatus6.70586829170916e-05
GO:0051248negative regulation of protein metabolic process7.63700270790536e-05
GO:0008021synaptic vesicle7.63700270790536e-05
GO:0019887protein kinase regulator activity8.00499495895361e-05
GO:0043226organelle8.26553474901764e-05
GO:0007163establishment and/or maintenance of cell polarity8.89723992926584e-05
GO:0043229intracellular organelle0.000140733398828741
GO:0006996organelle organization and biogenesis0.000141440384189975
GO:0048519negative regulation of biological process0.000163086275392608
GO:0043025cell soma0.000221870794344543
GO:0019207kinase regulator activity0.000222937724045669
GO:0031226intrinsic to plasma membrane0.000256283592696472
GO:0030159receptor signaling complex scaffold activity0.000259713722908952
GO:0048513organ development0.00027604822223895
GO:0030425dendrite0.000317005482636633
GO:0032947protein complex scaffold0.000392116652612512
GO:0015631tubulin binding0.000434867215621882
GO:0051128regulation of cellular component organization and biogenesis0.000465643828722441
GO:0007215glutamate signaling pathway0.000465643828722441
GO:0009892negative regulation of metabolic process0.000592315701652324
GO:0005887integral to plasma membrane0.000642634834106947
GO:0044430cytoskeletal part0.000735041808147006
GO:0019894kinesin binding0.00077130632065477
GO:0008017microtubule binding0.00101079337789295
GO:0030136clathrin-coated vesicle0.00106376615285904
GO:0045055regulated secretory pathway0.00144841610062207
GO:0044431Golgi apparatus part0.00148952086116649
GO:0000139Golgi membrane0.0015412146462981
GO:0012505endomembrane system0.00163451632020952
GO:0007218neuropeptide signaling pathway0.00177325011504058
GO:0042734presynaptic membrane0.00183099184926607
GO:0003779actin binding0.00214371155596119
GO:0006928cell motility0.00227375902564883
GO:0051674localization of cell0.00227375902564883
GO:0016812hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides0.00227864865597557
GO:0051641cellular localization0.00251317441237717
GO:0005875microtubule associated complex0.00266508657201481
GO:0030424axon0.00272576136131084
GO:0051010microtubule plus-end binding0.00272576136131084
GO:0030297transmembrane receptor protein tyrosine kinase activator activity0.00272576136131084
GO:0005078MAP-kinase scaffold activity0.00272576136131084
GO:0016477cell migration0.00298121402305956
GO:0000226microtubule cytoskeleton organization and biogenesis0.00352907957177657
GO:0030135coated vesicle0.00408213018131941
GO:0003001generation of a signal involved in cell-cell signaling0.00454661699894548
GO:0007269neurotransmitter secretion0.00483651981731951
GO:0051246regulation of protein metabolic process0.00487381307161995
GO:0051649establishment of cellular localization0.00490493729234046
GO:0030971receptor tyrosine kinase binding0.00502924929939348
GO:0005828kinetochore microtubule0.00502924929939348
GO:0022610biological adhesion0.00539048178996356
GO:0007155cell adhesion0.00539048178996356
GO:0019222regulation of metabolic process0.00566045210233311
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.00627938142265481
GO:0019198transmembrane receptor protein phosphatase activity0.00627938142265481
GO:0001505regulation of neurotransmitter levels0.00685724278682288
GO:0017124SH3 domain binding0.0072278715921299
GO:0030695GTPase regulator activity0.00766673766676316
GO:0018065protein-cofactor linkage0.0077731373112513
GO:0005200structural constituent of cytoskeleton0.00977442865904356
GO:0019904protein domain specific binding0.00977442865904356
GO:0016524latrotoxin receptor activity0.0106075277809639
GO:0030296protein tyrosine kinase activator activity0.0112552299957482
GO:0007018microtubule-based movement0.0115703401418131
GO:0050793regulation of developmental process0.0126384934951925
GO:0009966regulation of signal transduction0.013237548769626
GO:0007264small GTPase mediated signal transduction0.0136080790256467
GO:0045045secretory pathway0.0137597429228049
GO:0008066glutamate receptor activity0.0144267813414993
GO:0050770regulation of axonogenesis0.0144267813414993
GO:0031301integral to organelle membrane0.0144794849764786
GO:0007158neuron adhesion0.0146063834955669
GO:0001578microtubule bundle formation0.0146063834955669
GO:0019899enzyme binding0.0157987679119271
GO:0051258protein polymerization0.0159461568274189
GO:0031982vesicle0.0161800661997234
GO:0008134transcription factor binding0.0161800661997234
GO:0005085guanyl-nucleotide exchange factor activity0.0168059667178649
GO:0030705cytoskeleton-dependent intracellular transport0.0169836482925688
GO:0022836gated channel activity0.0177901140393509
GO:0005881cytoplasmic microtubule0.018251067615488
GO:0003730mRNA 3'-UTR binding0.018251067615488
GO:0031300intrinsic to organelle membrane0.0208250063540242
GO:0046903secretion0.0208250063540242
GO:0002062chondrocyte differentiation0.0226322752557863
GO:0008047enzyme activator activity0.0226322752557863
GO:0019932second-messenger-mediated signaling0.0239151923102481
GO:0044422organelle part0.0245234818656668
GO:0003924GTPase activity0.0270188420115136
GO:0001540beta-amyloid binding0.0272827096468203
GO:0005083small GTPase regulator activity0.0292386846782992
GO:0051056regulation of small GTPase mediated signal transduction0.0295275304745269
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0309693485069638
GO:0001764neuron migration0.0309693485069638
GO:0019717synaptosome0.0309693485069638
GO:0016247channel regulator activity0.0309693485069638
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0309693485069638
GO:0005246calcium channel regulator activity0.0316009420462899
GO:0031988membrane-bound vesicle0.0343176994981004
GO:0008373sialyltransferase activity0.0350552337150717
GO:0050767regulation of neurogenesis0.0350552337150717
GO:0019935cyclic-nucleotide-mediated signaling0.0357379919857634
GO:0045767regulation of anti-apoptosis0.0360377507174353
GO:0016358dendrite development0.0360377507174353
GO:0030516regulation of axon extension0.0360377507174353
GO:0044446intracellular organelle part0.0360377507174353
GO:0050877neurological system process0.0360377507174353
GO:0031410cytoplasmic vesicle0.0364945411492439
GO:0032940secretion by cell0.0385177209255228
GO:0004860protein kinase inhibitor activity0.0385836920973071
GO:0045761regulation of adenylate cyclase activity0.0409239831444474
GO:0003712transcription cofactor activity0.0415760387557223
GO:0051339regulation of lyase activity0.0428830180717856
GO:0031279regulation of cyclase activity0.0428830180717856
GO:0019210kinase inhibitor activity0.0428830180717856
GO:0003008system process0.0438511399644669



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
neuronal stem cell7.47e-108
Uber Anatomy
Ontology termp-valuen
central nervous system5.68e-10881
neural tube4.75e-10756
neural rod4.75e-10756
future spinal cord4.75e-10756
neural keel4.75e-10756
nervous system2.19e-10389
regional part of nervous system7.87e-9953
regional part of brain7.87e-9953
regional part of forebrain9.11e-8641
forebrain9.11e-8641
anterior neural tube9.11e-8641
future forebrain9.11e-8641
brain1.32e-8568
future brain1.32e-8568
telencephalon3.47e-8234
brain grey matter3.89e-8234
gray matter3.89e-8234
cerebral hemisphere5.49e-7732
regional part of telencephalon1.32e-7632
neural plate4.48e-7382
presumptive neural plate4.48e-7382
neurectoderm3.58e-6986
regional part of cerebral cortex1.84e-6522
neocortex2.85e-5920
pre-chordal neural plate3.06e-5861
ecto-epithelium7.17e-58104
cerebral cortex3.58e-5725
pallium3.58e-5725
ectoderm-derived structure1.82e-52171
ectoderm1.82e-52171
presumptive ectoderm1.82e-52171
adult organism2.47e-49114
structure with developmental contribution from neural crest2.08e-45132
organ system subdivision1.75e-37223
basal ganglion7.60e-279
nuclear complex of neuraxis7.60e-279
aggregate regional part of brain7.60e-279
collection of basal ganglia7.60e-279
cerebral subcortex7.60e-279
neural nucleus5.73e-269
nucleus of brain5.73e-269
tube1.86e-23192
posterior neural tube1.46e-2115
chordal neural plate1.46e-2115
telencephalic nucleus1.18e-207
gyrus1.59e-196
anatomical cluster4.50e-19373
brainstem4.03e-176
temporal lobe4.46e-176
limbic system7.55e-175
occipital lobe1.01e-165
parietal lobe1.30e-165
anatomical conduit1.56e-16240
segmental subdivision of hindbrain1.64e-1412
hindbrain1.64e-1412
presumptive hindbrain1.64e-1412
segmental subdivision of nervous system2.71e-1313
corpus striatum5.70e-134
striatum5.70e-134
ventral part of telencephalon5.70e-134
future corpus striatum5.70e-134
organ part2.73e-12218
epithelium4.35e-12306
cell layer7.32e-12309
frontal cortex7.54e-113
caudate-putamen4.21e-103
dorsal striatum4.21e-103
pons1.16e-093
spinal cord1.57e-093
dorsal region element1.57e-093
dorsum1.57e-093
medulla oblongata3.62e-093
myelencephalon3.62e-093
future myelencephalon3.62e-093
multi-tissue structure5.06e-09342
regional part of metencephalon3.48e-089
metencephalon3.48e-089
future metencephalon3.48e-089
germ layer3.64e-08560
germ layer / neural crest3.64e-08560
embryonic tissue3.64e-08560
presumptive structure3.64e-08560
germ layer / neural crest derived structure3.64e-08560
epiblast (generic)3.64e-08560
embryo3.69e-08592
embryonic structure5.20e-08564
developing anatomical structure5.88e-08581
amygdala6.46e-082
middle frontal gyrus8.41e-082
middle temporal gyrus8.98e-082
Ammon's horn9.28e-082
lobe parts of cerebral cortex9.28e-082
hippocampal formation9.28e-082
limbic lobe9.28e-082
caudate nucleus3.04e-072
future caudate nucleus3.04e-072
anatomical system5.06e-07624
dorsal plus ventral thalamus5.32e-072
locus ceruleus5.32e-072


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)
MA0003.114.7177
MA0004.10.00191132
MA0006.15.54178
MA0007.10.0103024
MA0009.10.191321
MA0014.131.4814
MA0017.15.56002e-07
MA0019.10.499776
MA0024.10.579643
MA0025.10.00962795
MA0027.10.429819
MA0028.14.10625e-05
MA0029.10.119621
MA0030.10.0117072
MA0031.10.00470435
MA0038.10.191964
MA0040.10.773826
MA0041.12.63229
MA0042.10.988746
MA0043.10.00183867
MA0046.10.0811989
MA0048.15.25117
MA0050.10.0191447
MA0051.10.292195
MA0052.10.477401
MA0055.17.72663
MA0056.10
MA0057.129.5526
MA0058.10.00021986
MA0059.10.186404
MA0060.11.09669e-05
MA0061.10.00342366
MA0063.10
MA0066.10.0103081
MA0067.10.0419852
MA0068.111.4949
MA0069.11.60384
MA0070.11.12385
MA0071.10.00215925
MA0072.10.451385
MA0073.188.1319
MA0074.10.168843
MA0076.11.06484e-11
MA0077.10.0481755
MA0078.10.350308
MA0081.10.00517247
MA0083.10.00226582
MA0084.10.249386
MA0087.10.211144
MA0088.12.02882
MA0089.10
MA0090.10.0218571
MA0091.10.0388117
MA0092.10.358043
MA0093.12.0262e-05
MA0095.10
MA0098.10
MA0100.10.00382596
MA0101.10.000354122
MA0103.10.00110273
MA0105.12.24296
MA0106.10.290051
MA0107.10.0019567
MA0108.20.0845114
MA0109.10
MA0111.10.328295
MA0113.10.0112866
MA0114.13.32851e-06
MA0115.10.000405533
MA0116.10.0444897
MA0117.10.757067
MA0119.10.00684639
MA0122.10.00444397
MA0124.10.429914
MA0125.10.247783
MA0130.10
MA0131.10.838394
MA0132.10
MA0133.10
MA0135.12.70799
MA0136.15.35787e-05
MA0139.11.60257
MA0140.10.000257168
MA0141.12.59045e-07
MA0142.10.0289298
MA0143.10.198345
MA0144.13.91842e-05
MA0145.10.000238594
MA0146.10.00695128
MA0147.11.04504
MA0148.10.112866
MA0149.117.5042
MA0062.22.46868e-14
MA0035.20.0124197
MA0039.29.6335
MA0138.20.852631
MA0002.23.58976e-09
MA0137.20.00431826
MA0104.22.34022
MA0047.20.0432939
MA0112.20.00548737
MA0065.20.239907
MA0150.17.80128e-08
MA0151.10
MA0152.10.8538
MA0153.10.202535
MA0154.10.000297303
MA0155.11.67766
MA0156.12.23595e-10
MA0157.10.00780596
MA0158.10
MA0159.10.0207527
MA0160.10.000174594
MA0161.10
MA0162.123.5685
MA0163.13.83027
MA0164.10.430656
MA0080.21.55706e-08
MA0018.20.00387809
MA0099.23.48515e-10
MA0079.2179.87
MA0102.20.0387817
MA0258.15.12652e-05
MA0259.10.977634
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
CTBP2#1488653.225162200993935.89293308213173e-161.12926979479772e-13
RAD21#58851711.400878794401135.24778122595753e-060.000160536913725184
SUZ12#23512853.370127672025591.1269426449015e-213.08106709138397e-19
ZNF263#101272201.431016740618953.42365937445953e-082.28767473710287e-06



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