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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.103554402440202

Latest revision as of 11:22, 17 September 2013


Full id: C401_Cardiac_pineal_occipital_globus_Hepatocyte_Osteoblast_hippocampus



Phase1 CAGE Peaks

Hg19::chr11:57367366..57367382,+p11@SERPING1
Hg19::chr11:57367449..57367472,+p10@SERPING1
Hg19::chr11:57382197..57382297,+p@chr11:57382197..57382297
+
Hg19::chr11:65200782..65200798,+p@chr11:65200782..65200798
+
Hg19::chr11:85195246..85195257,+p@chr11:85195246..85195257
+
Hg19::chr12:105258734..105258750,+p@chr12:105258734..105258750
+
Hg19::chr12:2912416..2912428,+p@chr12:2912416..2912428
+
Hg19::chr14:20811496..20811529,-p2@RPPH1
Hg19::chr14:69256272..69256281,-p@chr14:69256272..69256281
-
Hg19::chr17:1680785..1680829,+p@chr17:1680785..1680829
+
Hg19::chr19:41809934..41809945,+p@chr19:41809934..41809945
+
Hg19::chr19:45409845..45409890,+p2@APOE
Hg19::chr19:45412352..45412385,+p3@AJ249921
Hg19::chr19:45412497..45412513,+p5@AJ249921
Hg19::chr19:45412590..45412628,+p1@AJ249921
Hg19::chr19:6690736..6690743,-p@chr19:6690736..6690743
-
Hg19::chr22:36697071..36697092,-p37@MYH9
Hg19::chr2:189872602..189872638,+p14@COL3A1
Hg19::chr2:189876643..189876662,+p8@AF130082
Hg19::chr2:216253018..216253020,-p@chr2:216253018..216253020
-
Hg19::chr2:56149525..56149590,-p5@EFEMP1
Hg19::chr3:112324173..112324209,-p@chr3:112324173..112324209
-
Hg19::chr3:112324210..112324254,-p@chr3:112324210..112324254
-
Hg19::chr4:124323702..124323741,+p12@SPRY1
Hg19::chr5:40968730..40968733,+p@chr5:40968730..40968733
+
Hg19::chr6:132269474..132269484,-p@chr6:132269474..132269484
-


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:0008015blood circulation0.000419219703150404
GO:0003013circulatory system process0.000419219703150404
GO:0003008system process0.000419219703150404
GO:0032501multicellular organismal process0.00108973671533384
GO:0009653anatomical structure morphogenesis0.00198778520051913
GO:0009887organ morphogenesis0.00231233490456949
GO:0031252leading edge0.00450041737435283
GO:0042157lipoprotein metabolic process0.00536433127423976
GO:0048731system development0.00540490358575841
GO:0005319lipid transporter activity0.00540490358575841
GO:0043495protein anchor0.00540490358575841
GO:0050749apolipoprotein E receptor binding0.00540490358575841
GO:0005586collagen type III0.00540490358575841
GO:0006869lipid transport0.00780639350888681
GO:0048856anatomical structure development0.00780639350888681
GO:0048156tau protein binding0.00780639350888681
GO:0030220platelet formation0.00780639350888681
GO:0005826contractile ring0.00780639350888681
GO:0031232extrinsic to external side of plasma membrane0.00961154805122228
GO:0032154cleavage furrow0.00961154805122228
GO:0044421extracellular region part0.00961154805122228
GO:0007275multicellular organismal development0.00961154805122228
GO:0032153cell division site0.0108069435902759
GO:0043534blood vessel endothelial cell migration0.0108069435902759
GO:0030224monocyte differentiation0.0108069435902759
GO:0032155cell division site part0.0108069435902759
GO:0050793regulation of developmental process0.0124559386413484
GO:0048513organ development0.014530909143863
GO:0033344cholesterol efflux0.014530909143863
GO:0010092specification of organ identity0.0147832261379335
GO:0001759induction of an organ0.0147832261379335
GO:0050877neurological system process0.0147832261379335
GO:0031128induction0.0147832261379335
GO:0045168cell-cell signaling during cell fate commitment0.0147832261379335
GO:0042627chylomicron0.0147832261379335
GO:0031532actin cytoskeleton reorganization0.0147832261379335
GO:0050750low-density lipoprotein receptor binding0.0147832261379335
GO:0045471response to ethanol0.0147832261379335
GO:0042995cell projection0.0150458835817061
GO:0006707cholesterol catabolic process0.0150458835817061
GO:0016127sterol catabolic process0.0150458835817061
GO:0048168regulation of neuronal synaptic plasticity0.0150458835817061
GO:0001540beta-amyloid binding0.0163274240036984
GO:0032432actin filament bundle0.0164301906435854
GO:0005583fibrillar collagen0.0164301906435854
GO:0017127cholesterol transporter activity0.0164301906435854
GO:0001725stress fiber0.0164301906435854
GO:0007271synaptic transmission, cholinergic0.0168469259304954
GO:0043542endothelial cell migration0.0168469259304954
GO:0030516regulation of axon extension0.0168469259304954
GO:0032502developmental process0.0168974304224498
GO:0015248sterol transporter activity0.0168974304224498
GO:0033619membrane protein proteolysis0.0168974304224498
GO:0006509membrane protein ectodomain proteolysis0.0168974304224498
GO:0042632cholesterol homeostasis0.0181532546775641
GO:0000146microfilament motor activity0.0181532546775641
GO:0055092sterol homeostasis0.0181532546775641
GO:0005578proteinaceous extracellular matrix0.0181532546775641
GO:0030048actin filament-based movement0.0186374556962015
GO:0048167regulation of synaptic plasticity0.0186374556962015
GO:0006706steroid catabolic process0.0186374556962015
GO:0051262protein tetramerization0.0186374556962015
GO:0048675axon extension0.0186374556962015
GO:0055088lipid homeostasis0.0186374556962015
GO:0015918sterol transport0.0188485102725415
GO:0050803regulation of synapse structure and activity0.0188485102725415
GO:0030301cholesterol transport0.0188485102725415
GO:0042311vasodilation0.0190151302149179
GO:0001657ureteric bud development0.0190151302149179
GO:0032989cellular structure morphogenesis0.0190151302149179
GO:0000902cell morphogenesis0.0190151302149179
GO:0048869cellular developmental process0.02099236082885
GO:0030154cell differentiation0.02099236082885
GO:0043407negative regulation of MAP kinase activity0.0224387791240267
GO:0001656metanephros development0.0224387791240267
GO:0006810transport0.0231720613631511
GO:0050770regulation of axonogenesis0.0236731024067316
GO:0000302response to reactive oxygen species0.0242662892719579
GO:0051234establishment of localization0.0243968322304056
GO:0006958complement activation, classical pathway0.0245337484807454
GO:0008034lipoprotein binding0.0250940349738294
GO:0002573myeloid leukocyte differentiation0.0252749891205452
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0252749891205452
GO:0008092cytoskeletal protein binding0.0252749891205452
GO:0050900leukocyte migration0.025557807841472
GO:0000910cytokinesis0.0273925062569107
GO:0007267cell-cell signaling0.0273925062569107
GO:0005737cytoplasm0.0281269809152259
GO:0001822kidney development0.0283335906023209
GO:0051179localization0.0284490305427894
GO:0050767regulation of neurogenesis0.0284490305427894
GO:0007010cytoskeleton organization and biogenesis0.0284490305427894
GO:0002541activation of plasma proteins during acute inflammatory response0.0284490305427894
GO:0030027lamellipodium0.0284490305427894
GO:0006956complement activation0.0284490305427894
GO:0051015actin filament binding0.0284490305427894
GO:0001655urogenital system development0.0288275807188739
GO:0022603regulation of anatomical structure morphogenesis0.0288275807188739
GO:0022604regulation of cell morphogenesis0.0288275807188739
GO:0035150regulation of tube size0.0288275807188739
GO:0008360regulation of cell shape0.0288275807188739
GO:0050880regulation of blood vessel size0.0288275807188739
GO:0001726ruffle0.0289438204544674
GO:0003018vascular process in circulatory system0.0289438204544674
GO:0007611learning and/or memory0.0293322770254043
GO:0044448cell cortex part0.0297132878901067
GO:0044242cellular lipid catabolic process0.031389652619269
GO:0019897extrinsic to plasma membrane0.0320919334640991
GO:0009897external side of plasma membrane0.0320919334640991
GO:0016064immunoglobulin mediated immune response0.03243332931013
GO:0019724B cell mediated immunity0.0327684628976585
GO:0005581collagen0.0337190066691928
GO:0042158lipoprotein biosynthetic process0.0337379382312679
GO:0008305integrin complex0.0337379382312679
GO:0006469negative regulation of protein kinase activity0.0343558659292324
GO:0033673negative regulation of kinase activity0.0343558659292324
GO:0051348negative regulation of transferase activity0.0352511684169105
GO:0051259protein oligomerization0.0364113765646222
GO:0010033response to organic substance0.0364113765646222
GO:0005938cell cortex0.0372661420881728
GO:0046907intracellular transport0.0387880511005239
GO:0045165cell fate commitment0.0403088713670378
GO:0002253activation of immune response0.0403088713670378
GO:0002449lymphocyte mediated immunity0.0403603889076714
GO:0006629lipid metabolic process0.0403603889076714
GO:0007600sensory perception0.0403603889076714
GO:0065008regulation of biological quality0.0403603889076714
GO:0006959humoral immune response0.0404946883957359
GO:0008201heparin binding0.0404946883957359
GO:0002250adaptive immune response0.0404946883957359
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0404946883957359
GO:0030099myeloid cell differentiation0.0406227123295673
GO:0002443leukocyte mediated immunity0.0406227123295673
GO:0008203cholesterol metabolic process0.0406227123295673
GO:0002526acute inflammatory response0.0408351457951511
GO:0044267cellular protein metabolic process0.0420603796506103
GO:0035239tube morphogenesis0.042424566568245
GO:0050778positive regulation of immune response0.042424566568245
GO:0044260cellular macromolecule metabolic process0.042424566568245
GO:0007229integrin-mediated signaling pathway0.042424566568245
GO:0002684positive regulation of immune system process0.042424566568245
GO:0003002regionalization0.042424566568245
GO:0043086negative regulation of catalytic activity0.042424566568245
GO:0002521leukocyte differentiation0.0434321415613147
GO:0048518positive regulation of biological process0.0434321415613147
GO:0043405regulation of MAP kinase activity0.0443950312545569
GO:0016125sterol metabolic process0.044563210610377
GO:0051649establishment of cellular localization0.0453248758207287
GO:0019538protein metabolic process0.0454877976580822
GO:0050776regulation of immune response0.0455142610194365
GO:0007596blood coagulation0.0458239430195316
GO:0002682regulation of immune system process0.0458239430195316
GO:0051641cellular localization0.0459814820448974
GO:0050817coagulation0.0461252636618405
GO:0051240positive regulation of multicellular organismal process0.0468607423454333
GO:0007599hemostasis0.0468607423454333
GO:0019898extrinsic to membrane0.0471405369067976
GO:0016459myosin complex0.0471405369067976
GO:0043235receptor complex0.0475466257239393
GO:0002252immune effector process0.0475466257239393
GO:0005539glycosaminoglycan binding0.0475466257239393
GO:0007409axonogenesis0.0483130591651719
GO:0045087innate immune response0.0483130591651719
GO:0050789regulation of biological process0.0483130591651719
GO:0055074calcium ion homeostasis0.0483130591651719
GO:0006874cellular calcium ion homeostasis0.0483130591651719
GO:0030247polysaccharide binding0.0483130591651719
GO:0035295tube development0.048435221358892
GO:0006950response to stress0.0485090286102478
GO:0048667neuron morphogenesis during differentiation0.0485090286102478
GO:0006979response to oxidative stress0.0485090286102478
GO:0048812neurite morphogenesis0.0485090286102478
GO:0006875cellular metal ion homeostasis0.0488564508901125
GO:0055065metal ion homeostasis0.0488564508901125
GO:0005201extracellular matrix structural constituent0.0488564508901125
GO:0007389pattern specification process0.0489694878069881
GO:0050878regulation of body fluid levels0.049081178617439
GO:0000904cellular morphogenesis during differentiation0.0491915460187666
GO:0001871pattern binding0.0493006122010687
GO:0001525angiogenesis0.0497900101460195
GO:0044420extracellular matrix part0.0498271677129881
GO:0042060wound healing0.0498271677129881
GO:0050954sensory perception of mechanical stimulus0.0498271677129881
GO:0007605sensory perception of sound0.0498271677129881



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 organism5.58e-45114
neural tube1.28e-1256
neural rod1.28e-1256
future spinal cord1.28e-1256
neural keel1.28e-1256
central nervous system2.58e-1081
regional part of nervous system3.13e-1053
regional part of brain3.13e-1053
organ system subdivision2.61e-09223
brain3.28e-0968
future brain3.28e-0968
neural plate7.42e-0982
presumptive neural plate7.42e-0982
multi-cellular organism1.02e-08656
neurectoderm1.38e-0886
multi-tissue structure1.52e-08342
anatomical cluster1.69e-08373
nervous system2.51e-0889
brain grey matter2.52e-0834
gray matter2.52e-0834
structure with developmental contribution from neural crest2.90e-08132
telencephalon4.39e-0834
neural nucleus5.17e-089
nucleus of brain5.17e-089
regional part of forebrain1.25e-0741
forebrain1.25e-0741
anterior neural tube1.25e-0741
future forebrain1.25e-0741
tube4.37e-07192
brainstem4.41e-076
regional part of telencephalon6.02e-0732
cerebral hemisphere6.08e-0732
posterior neural tube7.31e-0715
chordal neural plate7.31e-0715
ecto-epithelium8.18e-07104
organ8.27e-07503
epithelium9.26e-07306


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)
MA0003.10.00551548
MA0004.10.122847
MA0006.10.180714
MA0007.10.36188
MA0009.10.46676
MA0014.10.000721098
MA0017.10.226532
MA0019.11.16376
MA0024.10.378349
MA0025.10.584598
MA0027.12.02165
MA0028.10.0539336
MA0029.11.02123
MA0030.10.384823
MA0031.10.33249
MA0038.10.546283
MA0040.10.399176
MA0041.10.133492
MA0042.10.369454
MA0043.11.17884
MA0046.10.457379
MA0048.10.217815
MA0050.10.370723
MA0051.10.183217
MA0052.10.402401
MA0055.10.389286
MA0056.10
MA0057.10.103816
MA0058.10.0742284
MA0059.10.54521
MA0060.10.0152409
MA0061.10.143203
MA0063.10
MA0066.10.546967
MA0067.10.753856
MA0068.10.361473
MA0069.10.454067
MA0070.10.44448
MA0071.10.160989
MA0072.10.44064
MA0073.10.0574575
MA0074.10.182721
MA0076.10.0815705
MA0077.10.434073
MA0078.10.252504
MA0081.10.927903
MA0083.10.473254
MA0084.10.931415
MA0087.10.438554
MA0088.10.0842883
MA0089.10
MA0090.11.53723
MA0091.10.124326
MA0092.10.338625
MA0093.10.0490184
MA0095.10
MA0098.10
MA0100.10.568627
MA0101.10.187837
MA0103.10.386056
MA0105.10.00962152
MA0106.10.61335
MA0107.10.112226
MA0108.20.330055
MA0109.10
MA0111.10.651585
MA0113.10.225587
MA0114.10.262046
MA0115.10.682809
MA0116.10.0276251
MA0117.10.499451
MA0119.10.236164
MA0122.10.522217
MA0124.10.644657
MA0125.10.568516
MA0130.10
MA0131.10.26595
MA0132.10
MA0133.10
MA0135.10.493123
MA0136.10.190708
MA0139.10.0450422
MA0140.10.48101
MA0141.10.54121
MA0142.10.828623
MA0143.10.640828
MA0144.10.448274
MA0145.10.104585
MA0146.10.465657
MA0147.10.284471
MA0148.10.425644
MA0149.10.153304
MA0062.20.0491752
MA0035.20.479916
MA0039.20.00190407
MA0138.20.253407
MA0002.20.330883
MA0137.20.206545
MA0104.20.183272
MA0047.20.59341
MA0112.21.34886
MA0065.20.0190901
MA0150.10.605252
MA0151.10
MA0152.10.491228
MA0153.10.553438
MA0154.10.283504
MA0155.10.396018
MA0156.10.458984
MA0157.10.286356
MA0158.10
MA0159.10.0287576
MA0160.10.448616
MA0161.10
MA0162.10.000113447
MA0163.10.0080283
MA0164.10.23445
MA0080.20.184213
MA0018.20.215022
MA0099.20.16368
MA0079.25.17791e-07
MA0102.20.967149
MA0258.10.688105
MA0259.10.126633
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


This analysis result is provided for C0 - C305 clusters.