Personal tools

Coexpression cluster:C268: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0.0954252957357428,0,0.272715235743603,0.253168552512612,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.283170292813857,0.27957974710499,0.554886091031534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.237692141113291,0.240940657106499,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.363288894383982,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.631994861971148,0.70681945923757,0.434701020002233,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.547067517346862,0.327158097282158,0.624996094995543,0.425956573949931,0,0,0,0,0,0,0,0,0,0,0,0,0,0.287205473226075,1.08830631966333,0.708546480623113,0.369842318828703,0.33496329655803,0.332468362080336,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0413820215904058,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.114741150775265,0,0,0,0,0,0,0,0,0,0,0,0,0,0.858278503551139,0.424466376862248,0,0,0,0,0.187268914901325,0,0,0.184054607617856,0,0,0,0,0,0,0.0986009078228607,0,0,0,0,0,0,0,0,0,0,0.332141639627736,0.556331571484542,0,0,0,0,0,0,0,0,0,0.79858969436259,0.749161121881861,0.48313114098195,0.480460503086891,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.493720985137221,0.222795072775063,0.319919697474494,0,0.603527336871469,0.640424737799617,0.657767094894883,0.988090040676487,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0929817338882301,0,0.116328982947523,0,0,0,0,0,0,0,0,0,0,0,0.0717850907807411,0,0,0,0,0,0,0,0,0,0,0,0.0890522440663336,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0373299241805104,0,0,0.0380625695285996,0.185552006688486,0,0,0,0,0,0,0,0,0.355257679842599,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.143629747351985,0.0697118989465167,0,0,0,0,0,0,0,0,0,0,0,0,0.0334876163089719,0,0,0,0,0,0.0584468268118252,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0435981622194311,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0917604244830311,0,0,0,0,0,0,0,0,0,0,0,0,0.0641946247847473,0,0,0,0,0,0,0,0,0,0.0443086593632396,0,0,0,0,0,0,0,0,0,0,0.0904423417827262,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.152177775803824,0.210071535945973,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0778384462202319,0.0484300422256687,0.135723143846782,0.0902761624927521,0,0,0,0,0,0,0,0.065867873206635,0.159437324174244,0,0,0,0,0,0,0,0,0.0988253147420914,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.150582174035777,0.0684524727462707,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0713494635703484,0.231925498757082,0.033520804106862,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0339876779246108,0,0,0,0,0,0,0,0,0
|full_id=C268_Mallassezderived_Urothelial_Gingival_Small_Bronchial_Tracheal_Prostate
|full_id=C268_Mallassezderived_Urothelial_Gingival_Small_Bronchial_Tracheal_Prostate
|gostat_on_coexpression_clusters=GO:0005610!laminin-5 complex!2.23558022420707e-06!3918;3914$GO:0008544!epidermis development!3.68581257411776e-05!5744;3918;3914$GO:0007398!ectoderm development!3.68581257411776e-05!5744;3918;3914$GO:0043256!laminin complex!3.68581257411776e-05!3918;3914$GO:0009888!tissue development!0.000241622122118908!5744;3918;3914$GO:0005605!basal lamina!0.00028975954818347!3918;3914$GO:0005604!basement membrane!0.000857750512404879!3918;3914$GO:0044420!extracellular matrix part!0.00235550148606838!3918;3914$GO:0007275!multicellular organismal development!0.00268383219890349!5744;3918;25914;3914$GO:0044421!extracellular region part!0.00310151907770258!5744;3918;3914$GO:0048513!organ development!0.00547554905699508!5744;3918;3914$GO:0032502!developmental process!0.00858513447901359!5744;3918;25914;3914$GO:0048731!system development!0.0119522547386036!5744;3918;3914$GO:0032501!multicellular organismal process!0.0119522547386036!5744;3918;25914;3914$GO:0005838!proteasome regulatory particle (sensu Eukaryota)!0.0119522547386036!5708$GO:0005578!proteinaceous extracellular matrix!0.0119522547386036!3918;3914$GO:0048856!anatomical structure development!0.0175600804050097!5744;3918;3914$GO:0007595!lactation!0.0175600804050097!5744$GO:0046058!cAMP metabolic process!0.0175600804050097!5744$GO:0007189!G-protein signaling, adenylate cyclase activating pathway!0.0280252688159154!5744$GO:0009187!cyclic nucleotide metabolic process!0.036034072684621!5744$GO:0043234!protein complex!0.0366964549910522!5708;3918;3914$GO:0048609!reproductive process in a multicellular organism!0.0366964549910522!5744$GO:0032504!multicellular organism reproduction!0.0366964549910522!5744$GO:0022610!biological adhesion!0.0366964549910522!3918;3914$GO:0007155!cell adhesion!0.0366964549910522!3918;3914$GO:0000502!proteasome complex (sensu Eukaryota)!0.0410003388770995!5708$GO:0008201!heparin binding!0.0410003388770995!3918$GO:0007565!female pregnancy!0.042175394935033!5744$GO:0007188!G-protein signaling, coupled to cAMP nucleotide second messenger!0.0422702018209267!5744$GO:0019933!cAMP-mediated signaling!0.0423582494144555!5744
|gostat_on_coexpression_clusters=GO:0005610!laminin-5 complex!2.23558022420707e-06!3918;3914$GO:0008544!epidermis development!3.68581257411776e-05!5744;3918;3914$GO:0007398!ectoderm development!3.68581257411776e-05!5744;3918;3914$GO:0043256!laminin complex!3.68581257411776e-05!3918;3914$GO:0009888!tissue development!0.000241622122118908!5744;3918;3914$GO:0005605!basal lamina!0.00028975954818347!3918;3914$GO:0005604!basement membrane!0.000857750512404879!3918;3914$GO:0044420!extracellular matrix part!0.00235550148606838!3918;3914$GO:0007275!multicellular organismal development!0.00268383219890349!5744;3918;25914;3914$GO:0044421!extracellular region part!0.00310151907770258!5744;3918;3914$GO:0048513!organ development!0.00547554905699508!5744;3918;3914$GO:0032502!developmental process!0.00858513447901359!5744;3918;25914;3914$GO:0048731!system development!0.0119522547386036!5744;3918;3914$GO:0032501!multicellular organismal process!0.0119522547386036!5744;3918;25914;3914$GO:0005838!proteasome regulatory particle (sensu Eukaryota)!0.0119522547386036!5708$GO:0005578!proteinaceous extracellular matrix!0.0119522547386036!3918;3914$GO:0048856!anatomical structure development!0.0175600804050097!5744;3918;3914$GO:0007595!lactation!0.0175600804050097!5744$GO:0046058!cAMP metabolic process!0.0175600804050097!5744$GO:0007189!G-protein signaling, adenylate cyclase activating pathway!0.0280252688159154!5744$GO:0009187!cyclic nucleotide metabolic process!0.036034072684621!5744$GO:0043234!protein complex!0.0366964549910522!5708;3918;3914$GO:0048609!reproductive process in a multicellular organism!0.0366964549910522!5744$GO:0032504!multicellular organism reproduction!0.0366964549910522!5744$GO:0022610!biological adhesion!0.0366964549910522!3918;3914$GO:0007155!cell adhesion!0.0366964549910522!3918;3914$GO:0000502!proteasome complex (sensu Eukaryota)!0.0410003388770995!5708$GO:0008201!heparin binding!0.0410003388770995!3918$GO:0007565!female pregnancy!0.042175394935033!5744$GO:0007188!G-protein signaling, coupled to cAMP nucleotide second messenger!0.0422702018209267!5744$GO:0019933!cAMP-mediated signaling!0.0423582494144555!5744

Revision as of 15:27, 12 September 2012


Full id: C268_Mallassezderived_Urothelial_Gingival_Small_Bronchial_Tracheal_Prostate



Phase1 CAGE Peaks

Hg19::chr12:28125659..28125672,-p1@PTHLH
Hg19::chr14:51955987..51955996,+p31@FRMD6
Hg19::chr14:51956090..51956101,+p32@FRMD6
Hg19::chr18:26736784..26736799,+p@chr18:26736784..26736799
+
Hg19::chr18:26736800..26736811,+p@chr18:26736800..26736811
+
Hg19::chr18:26736814..26736831,+p@chr18:26736814..26736831
+
Hg19::chr18:67715323..67715368,-p2@RTTN
Hg19::chr1:183155389..183155406,+p1@LAMC2
Hg19::chr1:183189986..183190012,+p@chr1:183189986..183190012
+
Hg19::chr1:183192299..183192310,+p@chr1:183192299..183192310
+
Hg19::chr1:183192330..183192349,+p@chr1:183192330..183192349
+
Hg19::chr1:183195929..183195945,+p@chr1:183195929..183195945
+
Hg19::chr1:183196792..183196807,+p@chr1:183196792..183196807
+
Hg19::chr1:183197647..183197676,+p@chr1:183197647..183197676
+
Hg19::chr1:183201372..183201407,+p@chr1:183201372..183201407
+
Hg19::chr1:183203526..183203539,+p@chr1:183203526..183203539
+
Hg19::chr1:183204745..183204775,+p@chr1:183204745..183204775
+
Hg19::chr1:183204785..183204796,+p@chr1:183204785..183204796
+
Hg19::chr1:183204800..183204830,+p@chr1:183204800..183204830
+
Hg19::chr1:183204832..183204840,+p@chr1:183204832..183204840
+
Hg19::chr1:183205642..183205677,+p@chr1:183205642..183205677
+
Hg19::chr1:183205712..183205723,+p@chr1:183205712..183205723
+
Hg19::chr1:183206514..183206566,+p@chr1:183206514..183206566
+
Hg19::chr1:183206565..183206612,-p@chr1:183206565..183206612
-
Hg19::chr1:183206616..183206643,-p@chr1:183206616..183206643
-
Hg19::chr1:183207431..183207488,+p@chr1:183207431..183207488
+
Hg19::chr1:183207499..183207519,+p@chr1:183207499..183207519
+
Hg19::chr1:183208494..183208511,+p9@LAMC2
Hg19::chr1:183208516..183208541,+p6@LAMC2
Hg19::chr1:183208540..183208573,-p@chr1:183208540..183208573
-
Hg19::chr1:183208543..183208558,+p8@LAMC2
Hg19::chr1:183208607..183208635,+p4@LAMC2
Hg19::chr1:183208643..183208654,+p10@LAMC2
Hg19::chr1:183208657..183208675,+p3@LAMC2
Hg19::chr1:183209165..183209207,+p@chr1:183209165..183209207
+
Hg19::chr1:183209229..183209250,+p@chr1:183209229..183209250
+
Hg19::chr1:183209265..183209312,-p@chr1:183209265..183209312
-
Hg19::chr1:183209335..183209346,-p@chr1:183209335..183209346
-
Hg19::chr1:183211988..183211991,+p@chr1:183211988..183211991
+
Hg19::chr1:183212294..183212340,+p2@LAMC2
Hg19::chr1:183212409..183212419,+p12@LAMC2
Hg19::chr1:183212478..183212492,+p7@LAMC2
Hg19::chr1:183212689..183212705,+p@chr1:183212689..183212705
+
Hg19::chr1:183212941..183212952,+p@chr1:183212941..183212952
+
Hg19::chr1:183212991..183213014,+p@chr1:183212991..183213014
+
Hg19::chr1:183213130..183213176,+p@chr1:183213130..183213176
+
Hg19::chr1:209790842..209790854,-p@chr1:209790842..209790854
-
Hg19::chr1:209826169..209826182,-p4@LAMB3
Hg19::chr3:184018352..184018374,+p3@PSMD2


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
0.0001304200680977750.0256875006414391285ECM-receptor interaction (KEGG):04512
0.0003192428343812150.03368011902721822133Toxoplasmosis (KEGG):05145
0.0002029028486685550.02568750064143912106Amoebiasis (KEGG):05146
0.0001304200680977750.0256875006414391285Small cell lung cancer (KEGG):05222
8.58329659590162e-050.0256875006414391269Alpha6-Beta4 Integrin Signaling Pathway (Wikipathways):WP244
0.0001699032356318450.0256875006414391297Cell junction organization (Reactome):REACT_20676



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:0005610laminin-5 complex2.23558022420707e-06
GO:0008544epidermis development3.68581257411776e-05
GO:0007398ectoderm development3.68581257411776e-05
GO:0043256laminin complex3.68581257411776e-05
GO:0009888tissue development0.000241622122118908
GO:0005605basal lamina0.00028975954818347
GO:0005604basement membrane0.000857750512404879
GO:0044420extracellular matrix part0.00235550148606838
GO:0007275multicellular organismal development0.00268383219890349
GO:0044421extracellular region part0.00310151907770258
GO:0048513organ development0.00547554905699508
GO:0032502developmental process0.00858513447901359
GO:0048731system development0.0119522547386036
GO:0032501multicellular organismal process0.0119522547386036
GO:0005838proteasome regulatory particle (sensu Eukaryota)0.0119522547386036
GO:0005578proteinaceous extracellular matrix0.0119522547386036
GO:0048856anatomical structure development0.0175600804050097
GO:0007595lactation0.0175600804050097
GO:0046058cAMP metabolic process0.0175600804050097
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0280252688159154
GO:0009187cyclic nucleotide metabolic process0.036034072684621
GO:0043234protein complex0.0366964549910522
GO:0048609reproductive process in a multicellular organism0.0366964549910522
GO:0032504multicellular organism reproduction0.0366964549910522
GO:0022610biological adhesion0.0366964549910522
GO:0007155cell adhesion0.0366964549910522
GO:0000502proteasome complex (sensu Eukaryota)0.0410003388770995
GO:0008201heparin binding0.0410003388770995
GO:0007565female pregnancy0.042175394935033
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0422702018209267
GO:0019933cAMP-mediated signaling0.0423582494144555



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
trunk3.03e-12216
multi-cellular organism1.40e-11659
mesenchyme2.52e-11238
entire embryonic mesenchyme2.52e-11238
anatomical system1.28e-10625
anatomical space1.45e-10104
anatomical group1.51e-10626
multilaminar epithelium2.05e-1082
surface structure6.66e-1095
organism subdivision1.23e-09365
trunk mesenchyme1.96e-09143
artery2.98e-0942
arterial blood vessel2.98e-0942
arterial system2.98e-0942
systemic artery3.02e-0933
systemic arterial system3.02e-0933
epithelium3.65e-09309
epithelial tube6.15e-09118
cell layer6.71e-09312
multi-tissue structure6.82e-09347
organ component layer1.76e-0857
endoderm-derived structure3.09e-08169
endoderm3.09e-08169
presumptive endoderm3.09e-08169
somite4.08e-0883
paraxial mesoderm4.08e-0883
presomitic mesoderm4.08e-0883
presumptive segmental plate4.08e-0883
trunk paraxial mesoderm4.08e-0883
presumptive paraxial mesoderm4.08e-0883
female organism5.10e-0841
vessel6.52e-0869
splanchnic layer of lateral plate mesoderm7.43e-0884
reproductive structure1.27e-0759
reproductive system1.27e-0759
blood vessel2.98e-0760
epithelial tube open at both ends2.98e-0760
blood vasculature2.98e-0760
vascular cord2.98e-0760
urinary system structure3.62e-0744
dermomyotome3.70e-0770
immaterial anatomical entity4.98e-07126
female reproductive organ5.03e-0737
female reproductive system5.03e-0737
extraembryonic membrane5.53e-0714
membranous layer5.53e-0714
renal system6.08e-0745
embryo7.71e-07612
thoracic segment of trunk9.66e-0752
Disease
Ontology termp-valuen
reproductive organ cancer7.84e-0829
female reproductive organ cancer1.60e-0727
squamous cell carcinoma4.56e-0714


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

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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C268&oldid=2137395"