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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C157_testicular_H9_testis_iPS_teratocarcinoma_colon_trachea
|full_id=C157_testicular_H9_testis_iPS_teratocarcinoma_colon_trachea
|gostat_on_coexpression_clusters=GO:0006355!regulation of transcription, DNA-dependent!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0016070!RNA metabolic process!0.0181646542156121!27287;57167;54457;11030;20;283150;2494;1993;8433;676$GO:0006351!transcription, DNA-dependent!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0032774!RNA biosynthetic process!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0003723!RNA binding!0.0181646542156121!1993;11030;55510;340168;166863$GO:0051177!meiotic sister chromatid cohesion!0.0181646542156121!50511$GO:0035093!spermatogenesis, exchange of chromosomal proteins!0.0181646542156121!50511$GO:0032377!regulation of intracellular lipid transport!0.0181646542156121!20$GO:0032380!regulation of intracellular sterol transport!0.0181646542156121!20$GO:0007066!female meiosis sister chromatid cohesion!0.0181646542156121!50511$GO:0000705!achiasmate meiosis I!0.0181646542156121!50511$GO:0032383!regulation of intracellular cholesterol transport!0.0181646542156121!20$GO:0045449!regulation of transcription!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0003676!nucleic acid binding!0.0181646542156121!27287;56164;57167;11030;55510;340168;50511;283150;84629;2494;1993;166863$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0006350!transcription!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0003702!RNA polymerase II transcription factor activity!0.0181646542156121!2494;8433;54457$GO:0010468!regulation of gene expression!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0031323!regulation of cellular metabolic process!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0005889!hydrogen:potassium-exchanging ATPase complex!0.0181646542156121!479$GO:0000802!transverse filament!0.0181646542156121!50511$GO:0042132!fructose-bisphosphatase activity!0.0181646542156121!2203$GO:0032374!regulation of cholesterol transport!0.0181646542156121!20$GO:0032371!regulation of sterol transport!0.0181646542156121!20$GO:0045132!meiotic chromosome segregation!0.0181646542156121!50511$GO:0032368!regulation of lipid transport!0.0181646542156121!20$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0192157860280854!27287;57167;54457;11030;20;50511;283150;2494;1993;8433;676$GO:0019222!regulation of metabolic process!0.0214597361942113!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0008900!hydrogen:potassium-exchanging ATPase activity!0.0214597361942113!479$GO:0043486!histone exchange!0.0214597361942113!50511$GO:0007141!male meiosis I!0.0214597361942113!50511$GO:0035092!sperm chromatin condensation!0.0214597361942113!50511$GO:0007143!female meiosis!0.0214597361942113!50511$GO:0007289!spermatid nuclear differentiation!0.024839339906988!50511$GO:0032365!intracellular lipid transport!0.024839339906988!20$GO:0032366!intracellular sterol transport!0.024839339906988!20$GO:0032367!intracellular cholesterol transport!0.024839339906988!20$GO:0000800!lateral element!0.024839339906988!50511$GO:0010467!gene expression!0.0294286409682944!27287;57167;54457;11030;20;283150;2494;1993;8433;676$GO:0043044!ATP-dependent chromatin remodeling!0.034508356674653!50511$GO:0007130!synaptonemal complex assembly!0.034508356674653!50511$GO:0050794!regulation of cellular process!0.0366681540950559!27287;57167;54457;20;50511;283150;2494;1993;676;8433$GO:0065007!biological regulation!0.0366681540950559!27287;57167;54457;20;50511;283150;2494;1993;8433;676;2814$GO:0007129!synapsis!0.0366681540950559!50511$GO:0007140!male meiosis!0.0366681540950559!50511$GO:0004331!fructose-2,6-bisphosphate 2-phosphatase activity!0.0401090432575329!2203$GO:0003730!mRNA 3'-UTR binding!0.0401090432575329!1993$GO:0019203!carbohydrate phosphatase activity!0.0419063281638503!2203$GO:0007062!sister chromatid cohesion!0.0419063281638503!50511$GO:0043190!ATP-binding cassette (ABC) transporter complex!0.0419063281638503!20$GO:0042623!ATPase activity, coupled!0.0419063281638503!55510;479;20$GO:0043283!biopolymer metabolic process!0.0462109027419868!27287;56164;57167;54457;11030;20;50511;283150;2494;1993;8433;676
|id=C157
|id=C157
}}
}}

Revision as of 17:35, 18 May 2012


Full id: C157_testicular_H9_testis_iPS_teratocarcinoma_colon_trachea



Phase1 CAGE Peaks

Hg19::chr10:135043493..135043510,+p2@UTF1
Hg19::chr10:135043674..135043682,+p9@UTF1
Hg19::chr10:135043690..135043701,+p4@UTF1
Hg19::chr10:135044076..135044090,+p8@UTF1
Hg19::chr10:135044170..135044188,+p7@UTF1
Hg19::chr10:135051353..135051367,+p1@VENTX
Hg19::chr10:98072001..98072012,-p@chr10:98072001..98072012
-
Hg19::chr10:98497275..98497286,+p@chr10:98497275..98497286
+
Hg19::chr11:118842467..118842477,+p1@FOXR1
Hg19::chr11:64136967..64136975,+p@chr11:64136967..64136975
+
Hg19::chr12:102133233..102133245,-p1@SYCP3
Hg19::chr12:31804934..31804953,-p@chr12:31804934..31804953
-
Hg19::chr12:31804958..31804974,-p@chr12:31804958..31804974
-
Hg19::chr12:4130254..4130285,+p@chr12:4130254..4130285
+
Hg19::chr12:7843093..7843102,-p@chr12:7843093..7843102
-
Hg19::chr12:7843145..7843150,-p@chr12:7843145..7843150
-
Hg19::chr12:7843168..7843173,-p@chr12:7843168..7843173
-
Hg19::chr12:7848349..7848359,-p2@GDF3
Hg19::chr12:7848364..7848378,-p1@GDF3
Hg19::chr12:7848400..7848403,-p3@GDF3
Hg19::chr12:7904213..7904218,-p2@CLEC4C
Hg19::chr12:7954930..7954932,+p@chr12:7954930..7954932
+
Hg19::chr12:8045030..8045044,+p5@NANOGP1
Hg19::chr12:8983864..8983875,-p2@A2ML1-AS1
Hg19::chr13:25254545..25254550,+p1@ATP12A
Hg19::chr13:25254693..25254710,+p2@ATP12A
Hg19::chr14:51360992..51360997,+p@chr14:51360992..51360997
+
Hg19::chr14:53299036..53299048,+p@chr14:53299036..53299048
+
Hg19::chr14:96152791..96152796,+p2@TCL1B
Hg19::chr14:99604394..99604433,-p@chr14:99604394..99604433
-
Hg19::chr15:35306088..35306093,+p@chr15:35306088..35306093
+
Hg19::chr15:89665804..89665808,-p@chr15:89665804..89665808
-
Hg19::chr15:98937858..98937881,-p@chr15:98937858..98937881
-
Hg19::chr16:24506492..24506513,-p1@BX538205
Hg19::chr16:70484243..70484248,-p@chr16:70484243..70484248
-
Hg19::chr16:71475936..71475963,-p@chr16:71475936..71475963
-
Hg19::chr16:9277969..9277994,+p@chr16:9277969..9277994
+
Hg19::chr17:19395753..19395759,+p@chr17:19395753..19395759
+
Hg19::chr19:13297435..13297437,+p@chr19:13297435..13297437
+
Hg19::chr19:42811002..42811015,+p@chr19:42811002..42811015
+
Hg19::chr19:46003039..46003051,+p6@PPM1N
Hg19::chr19:46003056..46003067,+p11@PPM1N
Hg19::chr19:46236688..46236701,+p1@ENST00000457052
Hg19::chr19:51883856..51883866,-p@chr19:51883856..51883866
-
Hg19::chr19:51883879..51883908,-p@chr19:51883879..51883908
-
Hg19::chr19:51883915..51883934,-p@chr19:51883915..51883934
-
Hg19::chr19:51883942..51883949,-p@chr19:51883942..51883949
-
Hg19::chr19:54168219..54168226,+p@chr19:54168219..54168226
+
Hg19::chr19:54290224..54290230,+p@chr19:54290224..54290230
+
Hg19::chr19:54290483..54290487,+p1@MIR371A
Hg19::chr19:55976108..55976119,-p@chr19:55976108..55976119
-
Hg19::chr1:155804359..155804366,-p@chr1:155804359..155804366
-
Hg19::chr1:155804376..155804383,-p@chr1:155804376..155804383
-
Hg19::chr1:155804425..155804436,-p@chr1:155804425..155804436
-
Hg19::chr1:156152062..156152074,+p@chr1:156152062..156152074
+
Hg19::chr1:200004156..200004159,+p@chr1:200004156..200004159
+
Hg19::chr1:200008057..200008103,+p1@BC080182
Hg19::chr1:65612630..65612670,+p@chr1:65612630..65612670
+
Hg19::chr1:92414952..92414965,+p1@BRDT
Hg19::chr20:50419112..50419117,-p10@SALL4
Hg19::chr21:45765639..45765654,-p@chr21:45765639..45765654
-
Hg19::chr21:45766204..45766222,-p@chr21:45766204..45766222
-
Hg19::chr21:47831204..47831214,+p@chr21:47831204..47831214
+
Hg19::chr22:17092528..17092530,+p@chr22:17092528..17092530
+
Hg19::chr22:27024930..27024945,+p@chr22:27024930..27024945
+
Hg19::chr2:27038042..27038048,+p@chr2:27038042..27038048
+
Hg19::chr3:109033438..109033449,-p@chr3:109033438..109033449
-
Hg19::chr3:109056727..109056765,+p2@ENST00000508178
Hg19::chr3:109128905..109128913,+p2@FLJ25363
Hg19::chr3:109128961..109129009,+p1@ENST00000489670
Hg19::chr3:115824886..115824897,-p@chr3:115824886..115824897
-
Hg19::chr3:194118687..194118692,-p4@GP5
Hg19::chr3:32838056..32838060,-p@chr3:32838056..32838060
-
Hg19::chr3:39268574..39268596,+p@chr3:39268574..39268596
+
Hg19::chr4:113571600..113571617,+p@chr4:113571600..113571617
+
Hg19::chr4:155702419..155702437,+p1@RBM46
Hg19::chr4:189030755..189030765,-p1@TRIML2
Hg19::chr4:2764786..2764789,+p@chr4:2764786..2764789
+
Hg19::chr5:150377663..150377680,-p@chr5:150377663..150377680
-
Hg19::chr5:176558815..176558850,+p@chr5:176558815..176558850
+
Hg19::chr6:2962186..2962206,-p21@SERPINB6
Hg19::chr6:38891759..38891774,+p@chr6:38891759..38891774
+
Hg19::chr6:38891781..38891789,+p@chr6:38891781..38891789
+
Hg19::chr6:38891794..38891799,+p@chr6:38891794..38891799
+
Hg19::chr6:38891807..38891809,+p@chr6:38891807..38891809
+
Hg19::chr6:74063949..74063957,-p3@DPPA5
Hg19::chr6:74104521..74104528,+p4@DDX43
Hg19::chr6:74104542..74104559,+p1@DDX43
Hg19::chr7:100293592..100293613,+p@chr7:100293592..100293613
+
Hg19::chr7:23749767..23749792,+p3@STK31
Hg19::chr7:23749832..23749845,+p2@STK31
Hg19::chr7:5447185..5447197,-p23@TNRC18
Hg19::chr7:6866868..6866875,-p3@CCZ1B
p4@CCZ1
Hg19::chr8:30244723..30244749,+p18@RBPMS
Hg19::chr8:42571671..42571675,-p@chr8:42571671..42571675
-
Hg19::chr9:101058489..101058493,+p@chr9:101058489..101058493
+
Hg19::chr9:139912749..139912794,-p8@ABCA2
Hg19::chr9:23779367..23779378,-p11@ELAVL2
Hg19::chr9:90692746..90692751,-p@chr9:90692746..90692751
-
Hg19::chr9:97402366..97402395,-p5@FBP1
Hg19::chrX:100548047..100548058,-p3@TAF7L
Hg19::chrX:100548065..100548075,-p4@TAF7L
Hg19::chrX:102965881..102965902,+p2@TMEM31
Hg19::chrX:103019822..103019825,-p@chrX:103019822..103019825
-
Hg19::chrX:103021870..103021902,-p@chrX:103021870..103021902
-
Hg19::chrX:114524275..114524308,+p1@LUZP4
Hg19::chrX:132568824..132568851,+p@chrX:132568824..132568851
+
Hg19::chrX:40482675..40482695,+p1@LOC347411
Hg19::chrX:40482706..40482715,+p2@LOC347411
Hg19::chrX:40482725..40482733,+p3@LOC347411


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:0006355regulation of transcription, DNA-dependent0.0181646542156121
GO:0016070RNA metabolic process0.0181646542156121
GO:0006351transcription, DNA-dependent0.0181646542156121
GO:0032774RNA biosynthetic process0.0181646542156121
GO:0003723RNA binding0.0181646542156121
GO:0051177meiotic sister chromatid cohesion0.0181646542156121
GO:0035093spermatogenesis, exchange of chromosomal proteins0.0181646542156121
GO:0032377regulation of intracellular lipid transport0.0181646542156121
GO:0032380regulation of intracellular sterol transport0.0181646542156121
GO:0007066female meiosis sister chromatid cohesion0.0181646542156121
GO:0000705achiasmate meiosis I0.0181646542156121
GO:0032383regulation of intracellular cholesterol transport0.0181646542156121
GO:0045449regulation of transcription0.0181646542156121
GO:0003676nucleic acid binding0.0181646542156121
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0181646542156121
GO:0006350transcription0.0181646542156121
GO:0003702RNA polymerase II transcription factor activity0.0181646542156121
GO:0010468regulation of gene expression0.0181646542156121
GO:0031323regulation of cellular metabolic process0.0181646542156121
GO:0005889hydrogen:potassium-exchanging ATPase complex0.0181646542156121
GO:0000802transverse filament0.0181646542156121
GO:0042132fructose-bisphosphatase activity0.0181646542156121
GO:0032374regulation of cholesterol transport0.0181646542156121
GO:0032371regulation of sterol transport0.0181646542156121
GO:0045132meiotic chromosome segregation0.0181646542156121
GO:0032368regulation of lipid transport0.0181646542156121
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0192157860280854
GO:0019222regulation of metabolic process0.0214597361942113
GO:0008900hydrogen:potassium-exchanging ATPase activity0.0214597361942113
GO:0043486histone exchange0.0214597361942113
GO:0007141male meiosis I0.0214597361942113
GO:0035092sperm chromatin condensation0.0214597361942113
GO:0007143female meiosis0.0214597361942113
GO:0007289spermatid nuclear differentiation0.024839339906988
GO:0032365intracellular lipid transport0.024839339906988
GO:0032366intracellular sterol transport0.024839339906988
GO:0032367intracellular cholesterol transport0.024839339906988
GO:0000800lateral element0.024839339906988
GO:0010467gene expression0.0294286409682944
GO:0043044ATP-dependent chromatin remodeling0.034508356674653
GO:0007130synaptonemal complex assembly0.034508356674653
GO:0050794regulation of cellular process0.0366681540950559
GO:0065007biological regulation0.0366681540950559
GO:0007129synapsis0.0366681540950559
GO:0007140male meiosis0.0366681540950559
GO:0004331fructose-2,6-bisphosphate 2-phosphatase activity0.0401090432575329
GO:0003730mRNA 3'-UTR binding0.0401090432575329
GO:0019203carbohydrate phosphatase activity0.0419063281638503
GO:0007062sister chromatid cohesion0.0419063281638503
GO:0043190ATP-binding cassette (ABC) transporter complex0.0419063281638503
GO:0042623ATPase activity, coupled0.0419063281638503
GO:0043283biopolymer metabolic process0.0462109027419868



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>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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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