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

Latest revision as of 10:02, 17 September 2013


Full id: C4_optic_corpus_substantia_medulla_spinal_thalamus_globus



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
0.0004554977353150560.048055011075738412204Endocytosis (KEGG):04144
1.23862032650889e-060.00039202333334006413133Tight junction (KEGG):04530
0.0003885784253031390.048055011075738410145Regulation of Actin Cytoskeleton (Wikipathways):WP51
5.85825024718095e-093.70827240646554e-0622265Axon guidance (Reactome):REACT_18266
0.0002557060392082340.048055011075738428728TNF alpha/NF-kB up reg. targets (Netpath):NetPath_9
0.0004462190184447490.0480550110757384420{SEPT2,21} (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 development7.62802929681149e-36
GO:0016020membrane2.93544116341676e-23
GO:0044425membrane part1.12056877507018e-18
GO:0044464cell part2.32723044079086e-18
GO:0008092cytoskeletal protein binding4.32292787472301e-18
GO:0005886plasma membrane5.98026358830576e-18
GO:0048856anatomical structure development5.98026358830576e-18
GO:0048731system development9.30468756701889e-18
GO:0005515protein binding2.2422557870013e-17
GO:0032502developmental process3.62912255220677e-17
GO:0005737cytoplasm4.57850014999345e-16
GO:0007275multicellular organismal development4.57850014999345e-16
GO:0022610biological adhesion4.83766074770396e-16
GO:0007155cell adhesion4.83766074770396e-16
GO:0032501multicellular organismal process2.83403626315056e-15
GO:0016021integral to membrane4.77698980630879e-14
GO:0031224intrinsic to membrane7.64322110847033e-14
GO:0003779actin binding1.34057695508074e-13
GO:0007010cytoskeleton organization and biogenesis1.28412345309015e-12
GO:0030054cell junction1.28412345309015e-12
GO:0007154cell communication1.33496346418656e-12
GO:0005856cytoskeleton7.39297960222583e-12
GO:0044459plasma membrane part3.57464514160195e-11
GO:0030695GTPase regulator activity4.41403003610958e-09
GO:0007267cell-cell signaling1.04750699867004e-08
GO:0016043cellular component organization and biogenesis5.05464150622618e-08
GO:0001508regulation of action potential1.26073996079989e-07
GO:0019226transmission of nerve impulse1.96956210256914e-07
GO:0044424intracellular part3.1144981328493e-07
GO:0008366axon ensheathment3.60090293850089e-07
GO:0007272ensheathment of neurons3.60090293850089e-07
GO:0048869cellular developmental process4.61019722862125e-07
GO:0030154cell differentiation4.61019722862125e-07
GO:0005624membrane fraction7.28547092261564e-07
GO:0005622intracellular1.11336892324559e-06
GO:0007165signal transduction2.58003912870551e-06
GO:0003008system process2.86933489209992e-06
GO:0000902cell morphogenesis2.89602304212069e-06
GO:0032989cellular structure morphogenesis2.89602304212069e-06
GO:0008289lipid binding1.00525834485181e-05
GO:0005083small GTPase regulator activity1.87782579033247e-05
GO:0000267cell fraction2.38036198604208e-05
GO:0005887integral to plasma membrane2.39204687317401e-05
GO:0009653anatomical structure morphogenesis2.78818810624975e-05
GO:0031226intrinsic to plasma membrane3.44756439181395e-05
GO:0030036actin cytoskeleton organization and biogenesis3.86091238949661e-05
GO:0050877neurological system process5.81309620220444e-05
GO:0030029actin filament-based process7.0142877408911e-05
GO:0022008neurogenesis7.55638654120488e-05
GO:0015630microtubule cytoskeleton0.000140666972199391
GO:0048699generation of neurons0.000140666972199391
GO:0015629actin cytoskeleton0.000309737077306256
GO:0048468cell development0.000309737077306256
GO:0005874microtubule0.000326495178106564
GO:0031175neurite development0.00037550194615179
GO:0007417central nervous system development0.000455983061479573
GO:0048858cell projection morphogenesis0.000502268000218197
GO:0032990cell part morphogenesis0.000502268000218197
GO:0030030cell projection organization and biogenesis0.000502268000218197
GO:0005516calmodulin binding0.00050450221588856
GO:0051179localization0.000516033877675488
GO:0005911intercellular junction0.000522118083651145
GO:0042552myelination0.000544804110195395
GO:0051056regulation of small GTPase mediated signal transduction0.000667733433204366
GO:0015631tubulin binding0.000734872847573226
GO:0048667neuron morphogenesis during differentiation0.000766991793937902
GO:0048812neurite morphogenesis0.000766991793937902
GO:0007268synaptic transmission0.000812211874055458
GO:0006629lipid metabolic process0.00090423506924232
GO:0048666neuron development0.00092771639605446
GO:0008017microtubule binding0.00103190304689554
GO:0000904cellular morphogenesis during differentiation0.00105084401298936
GO:0031109microtubule polymerization or depolymerization0.001352921350636
GO:0044430cytoskeletal part0.0014587372483156
GO:0042995cell projection0.00168058975947955
GO:0007158neuron adhesion0.00174997744229423
GO:0007242intracellular signaling cascade0.00224815269444086
GO:0016044membrane organization and biogenesis0.00228588017223452
GO:0030182neuron differentiation0.00236883755235154
GO:0007409axonogenesis0.00281923398533642
GO:0009966regulation of signal transduction0.0028507791390555
GO:0005875microtubule associated complex0.00289534133549436
GO:0007265Ras protein signal transduction0.00308771772176905
GO:0005826contractile ring0.00349296978728758
GO:0004572mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity0.00349296978728758
GO:0031114regulation of microtubule depolymerization0.00349296978728758
GO:0007026negative regulation of microtubule depolymerization0.00349296978728758
GO:0007167enzyme linked receptor protein signaling pathway0.00349296978728758
GO:0050953sensory perception of light stimulus0.00353248176073426
GO:0007601visual perception0.00353248176073426
GO:0007019microtubule depolymerization0.00399693303361887
GO:0031111negative regulation of microtubule polymerization or depolymerization0.00399693303361887
GO:0005096GTPase activator activity0.00406378529841967
GO:0005085guanyl-nucleotide exchange factor activity0.00436596981345683
GO:0007017microtubule-based process0.00510088471314355
GO:0010324membrane invagination0.00510088471314355
GO:0006897endocytosis0.00510088471314355
GO:0006996organelle organization and biogenesis0.00520148931359077
GO:0004385guanylate kinase activity0.00599123697206624
GO:0008047enzyme activator activity0.00606969145534406
GO:0004112cyclic-nucleotide phosphodiesterase activity0.00625060272493628
GO:0000226microtubule cytoskeleton organization and biogenesis0.00665185054151881
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.00789700541093445
GO:0005783endoplasmic reticulum0.00824331964102461
GO:0005594collagen type IX0.00852886210856089
GO:0031110regulation of microtubule polymerization or depolymerization0.00869377254360897
GO:0006928cell motility0.00907526081278021
GO:0051674localization of cell0.00907526081278021
GO:0006810transport0.0100964059358843
GO:0016337cell-cell adhesion0.0110983645959851
GO:0019899enzyme binding0.0113880101567791
GO:0007043intercellular junction assembly0.0113880101567791
GO:0065007biological regulation0.0114345341354466
GO:0006631fatty acid metabolic process0.0146814173154532
GO:0032155cell division site part0.0153477263882897
GO:0032153cell division site0.0153477263882897
GO:0019717synaptosome0.0180818691619343
GO:0005794Golgi apparatus0.0200991953459061
GO:0051234establishment of localization0.0206456433123382
GO:0032787monocarboxylic acid metabolic process0.0207817160341849
GO:0043228non-membrane-bound organelle0.0207817160341849
GO:0043232intracellular non-membrane-bound organelle0.0207817160341849
GO:0048519negative regulation of biological process0.0207817160341849
GO:0006936muscle contraction0.0207817160341849
GO:0003012muscle system process0.0207817160341849
GO:0005099Ras GTPase activator activity0.0207817160341849
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0207817160341849
GO:0045216intercellular junction assembly and maintenance0.0213351275437189
GO:0005543phospholipid binding0.0213351275437189
GO:0005319lipid transporter activity0.0220484157385909
GO:0009062fatty acid catabolic process0.0223540480697841
GO:0048523negative regulation of cellular process0.0237779638994941
GO:0006461protein complex assembly0.0240243512312942
GO:0012505endomembrane system0.0240345216205105
GO:0051094positive regulation of developmental process0.0254473508634744
GO:0051128regulation of cellular component organization and biogenesis0.0258091686328295
GO:0006869lipid transport0.0258091686328295
GO:0007264small GTPase mediated signal transduction0.0272904328254707
GO:0044255cellular lipid metabolic process0.0272904328254707
GO:0008081phosphoric diester hydrolase activity0.0286191410127116
GO:0001726ruffle0.0294360896998962
GO:0005593FACIT collagen0.0307384931403469
GO:0031252leading edge0.0309639114925554
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0338883379554932
GO:0030286dynein complex0.0338883379554932
GO:0051261protein depolymerization0.0364955915398225
GO:0044446intracellular organelle part0.040161636986754
GO:0007266Rho protein signal transduction0.0401874109204143
GO:0001609adenosine receptor activity, G-protein coupled0.0401874109204143
GO:0015018galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity0.0401874109204143
GO:0001578microtubule bundle formation0.0401874109204143
GO:0044422organelle part0.0414734264661
GO:0007422peripheral nervous system development0.0414789730862933
GO:0007028cytoplasm organization and biogenesis0.0414789730862933
GO:0016477cell migration0.0414789730862933
GO:0005070SH3/SH2 adaptor activity0.0428232216115219
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0435394068095353
GO:0043229intracellular organelle0.0475275948903329
GO:0043226organelle0.0482981557627676
GO:0042135neurotransmitter catabolic process0.0496037695751093



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 tube2.24e-11856
neural rod2.24e-11856
future spinal cord2.24e-11856
neural keel2.24e-11856
regional part of nervous system5.73e-10753
regional part of brain5.73e-10753
central nervous system2.72e-9581
brain8.27e-9068
future brain8.27e-9068
nervous system2.10e-8989
neural plate7.22e-8782
presumptive neural plate7.22e-8782
regional part of forebrain4.21e-8641
forebrain4.21e-8641
anterior neural tube4.21e-8641
future forebrain4.21e-8641
brain grey matter4.91e-8434
gray matter4.91e-8434
telencephalon7.26e-8434
neurectoderm1.87e-8286
regional part of telencephalon3.07e-7632
cerebral hemisphere7.75e-7632
adult organism2.91e-70114
ecto-epithelium9.42e-67104
pre-chordal neural plate5.03e-6461
regional part of cerebral cortex4.02e-5822
structure with developmental contribution from neural crest4.41e-56132
cerebral cortex7.08e-5125
pallium7.08e-5125
neocortex9.41e-5120
ectoderm-derived structure5.77e-45171
ectoderm5.77e-45171
presumptive ectoderm5.77e-45171
neural nucleus4.33e-369
nucleus of brain4.33e-369
basal ganglion2.95e-359
nuclear complex of neuraxis2.95e-359
aggregate regional part of brain2.95e-359
collection of basal ganglia2.95e-359
cerebral subcortex2.95e-359
organ system subdivision2.38e-32223
posterior neural tube2.09e-3115
chordal neural plate2.09e-3115
tube1.39e-28192
telencephalic nucleus4.07e-287
brainstem2.46e-256
segmental subdivision of nervous system1.44e-2413
gyrus1.72e-236
anatomical conduit4.59e-21240
segmental subdivision of hindbrain6.15e-2112
hindbrain6.15e-2112
presumptive hindbrain6.15e-2112
limbic system5.05e-205
organ part5.54e-17218
epithelium1.07e-16306
anatomical cluster1.27e-16373
cell layer1.92e-16309
corpus striatum6.02e-164
striatum6.02e-164
ventral part of telencephalon6.02e-164
future corpus striatum6.02e-164
temporal lobe4.10e-146
pons1.30e-133
medulla oblongata1.75e-133
myelencephalon1.75e-133
future myelencephalon1.75e-133
spinal cord2.54e-133
dorsal region element2.54e-133
dorsum2.54e-133
occipital lobe3.82e-135
parietal lobe4.07e-135
frontal cortex1.59e-123
caudate-putamen2.47e-123
dorsal striatum2.47e-123
multi-tissue structure5.73e-12342
regional part of metencephalon3.49e-119
metencephalon3.49e-119
future metencephalon3.49e-119
multi cell component structure4.85e-102
neuron projection bundle4.85e-102
dorsal plus ventral thalamus6.02e-102
thalamic complex6.02e-102
globus pallidus8.48e-102
pallidum8.48e-102
locus ceruleus1.05e-092
brainstem nucleus1.05e-092
hindbrain nucleus1.05e-092
Ammon's horn2.87e-092
lobe parts of cerebral cortex2.87e-092
hippocampal formation2.87e-092
limbic lobe2.87e-092
middle temporal gyrus3.99e-092
organ4.84e-09503
middle frontal gyrus6.50e-092
caudate nucleus7.04e-092
future caudate nucleus7.04e-092
amygdala7.33e-092
meninx2.14e-082
membrane organ2.14e-082
meningeal cluster2.14e-082


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)
MA0003.17.80307
MA0004.10.0256738
MA0006.10.0745352
MA0007.11.77087
MA0009.10.00584446
MA0014.12.30311
MA0017.10.0574433
MA0019.10.168741
MA0024.11.05597
MA0025.10.0555989
MA0027.10.635575
MA0028.14.4075e-11
MA0029.10.080962
MA0030.12.24411
MA0031.10.658231
MA0038.10.0530129
MA0040.12.17064
MA0041.10.403563
MA0042.11.97632
MA0043.10.0568993
MA0046.10.000101224
MA0048.16.86893
MA0050.10.00044446
MA0051.10.0114298
MA0052.10.0269097
MA0055.116.1387
MA0056.10
MA0057.11.71572
MA0058.10.159177
MA0059.10.148163
MA0060.13.06868e-12
MA0061.10.0996827
MA0063.10
MA0066.10.0011211
MA0067.10.24041
MA0068.10.513434
MA0069.10.0372808
MA0070.11.58261
MA0071.10.0573884
MA0072.10.128129
MA0073.124.6906
MA0074.10.085337
MA0076.10
MA0077.111.2179
MA0078.18.50037
MA0081.10.000262772
MA0083.10.0686297
MA0084.11.98477
MA0087.11.60421
MA0088.11.97882
MA0089.10
MA0090.10.00456697
MA0091.12.34843
MA0092.10.16204
MA0093.10.00586589
MA0095.10
MA0098.10
MA0100.10.00115013
MA0101.10.000258836
MA0103.10.019213
MA0105.10.302075
MA0106.10.00569902
MA0107.10.000138874
MA0108.21.35081e-06
MA0109.10
MA0111.12.27736
MA0113.14.31133
MA0114.10.0416945
MA0115.11.03106
MA0116.10.114926
MA0117.10.030467
MA0119.12.26677
MA0122.10.407743
MA0124.10.313949
MA0125.10.101696
MA0130.10
MA0131.10.0708022
MA0132.10
MA0133.10
MA0135.10.189652
MA0136.12.16325e-08
MA0139.17.17631
MA0140.10.0596426
MA0141.10.00338777
MA0142.13.10482
MA0143.13.98491
MA0144.10.0280039
MA0145.112.9001
MA0146.10.753337
MA0147.10.547447
MA0148.12.67635
MA0149.10.0156689
MA0062.20
MA0035.20.000643481
MA0039.23.4764e-05
MA0138.22.18629
MA0002.26.22248
MA0137.20.00301691
MA0104.21.25444
MA0047.21.34466
MA0112.22.31433
MA0065.24.03269
MA0150.10.00767063
MA0151.10
MA0152.10.0408758
MA0153.10.0508909
MA0154.17.68053
MA0155.16.3976
MA0156.12.89298e-16
MA0157.11.75938
MA0158.10
MA0159.10.0823907
MA0160.10.13765
MA0161.10
MA0162.11.28093
MA0163.11.05939
MA0164.10.400322
MA0080.21.02556e-13
MA0018.20.00242416
MA0099.24.89865e-08
MA0079.29.11966
MA0102.20.00235531
MA0258.10.566286
MA0259.10.469844
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


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