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Coexpression cluster:C216: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0001649!osteoblast differentiation!0.0100475295887183!121340;860$GO:0001503!ossification!0.0272192921654796!121340;860$GO:0031214!biomineral formation!0.0272192921654796!121340;860$GO:0046849!bone remodeling!0.0272192921654796!121340;860$GO:0048771!tissue remodeling!0.0272192921654796!121340;860$GO:0033188!sphingomyelin synthase activity!0.0272192921654796!166929$GO:0047493!ceramide cholinephosphotransferase activity!0.0272192921654796!166929$GO:0006686!sphingomyelin biosynthetic process!0.0357190113645948!166929$GO:0004237!membrane dipeptidase activity!0.0380935499990268!1800$GO:0019228!generation of action potential!0.0380935499990268!10242$GO:0005792!microsome!0.0384084890398877!260293;1800$GO:0042598!vesicular fraction!0.0384084890398877!260293;1800
|gostat_on_coexpression_clusters=GO:0001649!osteoblast differentiation!0.0100475295887183!121340;860$GO:0001503!ossification!0.0272192921654796!121340;860$GO:0031214!biomineral formation!0.0272192921654796!121340;860$GO:0046849!bone remodeling!0.0272192921654796!121340;860$GO:0048771!tissue remodeling!0.0272192921654796!121340;860$GO:0033188!sphingomyelin synthase activity!0.0272192921654796!166929$GO:0047493!ceramide cholinephosphotransferase activity!0.0272192921654796!166929$GO:0006686!sphingomyelin biosynthetic process!0.0357190113645948!166929$GO:0004237!membrane dipeptidase activity!0.0380935499990268!1800$GO:0019228!generation of action potential!0.0380935499990268!10242$GO:0005792!microsome!0.0384084890398877!260293;1800$GO:0042598!vesicular fraction!0.0384084890398877!260293;1800
|id=C216
|id=C216
|ontology_enrichment_celltype=CL:0000153!6.12e-07!9;CL:0000447!6.12e-07!9
|ontology_enrichment_disease=DOID:162!7.43e-12!235;DOID:14566!1.43e-11!239;DOID:0050686!1.74e-07!137;DOID:1240!1.95e-07!39;DOID:2531!2.29e-07!51;DOID:0060083!2.29e-07!51;DOID:0050687!2.91e-07!143
|ontology_enrichment_uberon=
}}
}}

Revision as of 14:20, 21 May 2012


Full id: C216_osteosarcoma_Smooth_Mesenchymal_large_neuroectodermal_acute_CD34



Phase1 CAGE Peaks

Hg19::chr10:24754616..24754639,+p@chr10:24754616..24754639
+
Hg19::chr11:124482705..124482719,+p@chr11:124482705..124482719
+
Hg19::chr12:124298058..124298065,+p@chr12:124298058..124298065
+
Hg19::chr12:53729525..53729541,-p5@SP7
Hg19::chr12:53729546..53729565,-p4@SP7
Hg19::chr12:53730126..53730146,-p1@SP7
Hg19::chr12:91395963..91395968,-p@chr12:91395963..91395968
-
Hg19::chr12:91398742..91398768,-p1@EPYC
Hg19::chr12:91398796..91398808,-p2@EPYC
Hg19::chr14:70656111..70656132,-p6@SLC8A3
Hg19::chr14:70656139..70656147,-p9@SLC8A3
Hg19::chr16:65210813..65210818,-p3@AL110259
Hg19::chr16:69963162..69963192,+p@chr16:69963162..69963192
+
Hg19::chr16:89687120..89687166,+p3@DPEP1
Hg19::chr17:16342343..16342358,+p1@C17orf76-AS1
Hg19::chr17:16342617..16342648,+p3@C17orf76-AS1
Hg19::chr17:16948336..16948342,-p@chr17:16948336..16948342
-
Hg19::chr17:17109452..17109461,-p4@PLD6
Hg19::chr17:17109579..17109683,-p2@PLD6
Hg19::chr17:17140420..17140429,-p3@FLCN
Hg19::chr17:40998129..40998141,+p@chr17:40998129..40998141
+
Hg19::chr17:40998185..40998200,+p@chr17:40998185..40998200
+
Hg19::chr17:40998201..40998206,+p@chr17:40998201..40998206
+
Hg19::chr19:14674382..14674403,+p@chr19:14674382..14674403
+
Hg19::chr19:18543312..18543351,+p@chr19:18543312..18543351
+
Hg19::chr19:18543503..18543510,+p@chr19:18543503..18543510
+
Hg19::chr1:170242760..170242801,-p1@LOC284688
Hg19::chr1:199050098..199050109,-p@chr1:199050098..199050109
-
Hg19::chr1:40916251..40916260,+p7@ZNF643
Hg19::chr1:47501378..47501387,+p12@CYP4X1
Hg19::chr1:47501412..47501425,+p9@CYP4X1
Hg19::chr1:47501441..47501449,+p11@CYP4X1
Hg19::chr1:47501501..47501514,+p8@CYP4X1
Hg19::chr21:17340298..17340318,+p@chr21:17340298..17340318
+
Hg19::chr21:26890785..26890790,-p2@ENST00000419694
Hg19::chr21:45874953..45874970,-p@chr21:45874953..45874970
-
Hg19::chr2:53859899..53859908,-p@chr2:53859899..53859908
-
Hg19::chr3:124485247..124485272,-p@chr3:124485247..124485272
-
Hg19::chr3:144069136..144069152,+p@chr3:144069136..144069152
+
Hg19::chr3:144069187..144069198,+p@chr3:144069187..144069198
+
Hg19::chr3:178525080..178525086,+p10@KCNMB2
Hg19::chr4:108815559..108815563,+p11@SGMS2
Hg19::chr6:160023967..160023971,+p@chr6:160023967..160023971
+
Hg19::chr6:168333044..168333049,+p36@MLLT4
Hg19::chr6:168333065..168333071,+p33@MLLT4
Hg19::chr6:169126213..169126247,+p@chr6:169126213..169126247
+
Hg19::chr6:33145331..33145378,-p@chr6:33145331..33145378
-
Hg19::chr6:36733547..36733556,-p@chr6:36733547..36733556
-
Hg19::chr6:36733562..36733582,-p@chr6:36733562..36733582
-
Hg19::chr6:36733583..36733590,-p@chr6:36733583..36733590
-
Hg19::chr6:36733594..36733607,-p@chr6:36733594..36733607
-
Hg19::chr6:36737372..36737379,+p@chr6:36737372..36737379
+
Hg19::chr6:36737414..36737422,+p@chr6:36737414..36737422
+
Hg19::chr6:44447751..44447754,+p@chr6:44447751..44447754
+
Hg19::chr6:45296191..45296203,+p13@RUNX2
Hg19::chr6:45296266..45296277,+p34@RUNX2
Hg19::chr6:45296391..45296400,+p52@RUNX2
Hg19::chr6:45297658..45297701,-p@chr6:45297658..45297701
-
Hg19::chr6:45352470..45352474,+p@chr6:45352470..45352474
+
Hg19::chr8:117778736..117778808,+p1@UTP23
Hg19::chr8:120651826..120651840,-p@chr8:120651826..120651840
-
Hg19::chr8:122398817..122398818,-p@chr8:122398817..122398818
-
Hg19::chr8:122442654..122442661,-p@chr8:122442654..122442661
-
Hg19::chr8:122442669..122442674,-p@chr8:122442669..122442674
-
Hg19::chr8:122442675..122442684,-p@chr8:122442675..122442684
-
Hg19::chr8:38470503..38470508,+p@chr8:38470503..38470508
+
Hg19::chr8:52721907..52721937,-p2@PXDNL
Hg19::chr9:116398779..116398800,+p@chr9:116398779..116398800
+
Hg19::chr9:95186583..95186648,-p1@OMD


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:0001649osteoblast differentiation0.0100475295887183
GO:0001503ossification0.0272192921654796
GO:0031214biomineral formation0.0272192921654796
GO:0046849bone remodeling0.0272192921654796
GO:0048771tissue remodeling0.0272192921654796
GO:0033188sphingomyelin synthase activity0.0272192921654796
GO:0047493ceramide cholinephosphotransferase activity0.0272192921654796
GO:0006686sphingomyelin biosynthetic process0.0357190113645948
GO:0004237membrane dipeptidase activity0.0380935499990268
GO:0019228generation of action potential0.0380935499990268
GO:0005792microsome0.0384084890398877
GO:0042598vesicular fraction0.0384084890398877



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><br>disease_data<br>

Cell Type
Ontology termp-valuen
GAG secreting cell6.12e-079
carbohydrate secreting cell6.12e-079
Disease
Ontology termp-valuen
cancer7.43e-12235
disease of cellular proliferation1.43e-11239
organ system cancer1.74e-07137
leukemia1.95e-0739
hematologic cancer2.29e-0751
immune system cancer2.29e-0751
cell type cancer2.91e-07143


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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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