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Coexpression cluster:C114: Difference between revisions

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|tf_chipseq_enrich=POU5F1#5460;4:8.18144393785136:0.0015578912661477:0.00989085750426744
|tf_chipseq_enrich=POU5F1#5460;4:8.18144393785136:0.0015578912661477:0.00989085750426744
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|tfbs_overrepresentation_for_novel_motifs=0.111764,0.125374,0.0321614,0.509845,0.459187,0.355289,0.447537,0.347683,0.195469,0.10663,0.0250687,0.409968,0.0434016,0.270043,0.884465,0.114851,0.0504639,1.04022,0.0168626,0.173634,0.893439,0.373332,0.0140259,0.326442,0.392295,0.685612,0.514312,0.0341326,0.607583,0.441969,0.212599,0.0666204,0.578019,1.91111,0.0210741,0.41607,8.45832e-07,0.0161896,0.254161,0.0926212,2.16447,0.176234,0.134038,0.116782,0.131043,0.0976986,0.0991314,0.0890183,0.307022,0.0829956,0.339703,0.328434,0.150212,0.497161,0.0657275,0.0896167,1.58593,0.323979,0.623899,0.0610343,0.221308,0.30515,0.260513,0.240053,0.00571582,0.00528744,0.670401,0.313039,0.551993,0.593554,0.45943,0.172799,0.00154109,0.231752,0.0145028,0.0230606,0.506704,0.0346042,0.0602995,0.261042,0.0326104,0.0397796,0.349386,0.0340523,0.0492271,0.000123911,1.0942e-05,1.15674,0.402659,0.386773,0.14286,0.0419697,0.193353,0.519157,0.0129341,0.396705,2.33131,0.243985,1.49405,0.262688,0.985731,0.187105,0.0219145,0.289171,0.026336,0.00878742,0.0457425,0.400476,0.279436,0.0174803,0.634884,0.233576,0.301164,0.0290305,0.119414,0.090968,0.000310345,0.209785,0.188675,0.257427,0.223825,0.598051,0.0782115,0.379369,0.176534,0.101482,0.427233,0.0775569,0.0770975,1.66555,0.0421464,0.219398,0.0824878,0.758517,0.149505,0.488587,0.0705978,0.215297,0.801523,0.774697,0.42769,0.357386,0.432714,0.734831,0.0812931,1.30884,1.28824,0.631764,0.169302,0.00212825,0.0356007,2.26065e-09,0.16314,0.0563896,0.457204,0.224561,0.362887,0.629221,0.00722765,0.129059,0.721301,0.148579,0.54159,0.538331,1.47547,0.347332,0.24613,0.178621,2.60484e-05
}}
}}

Revision as of 13:28, 26 November 2012


Full id: C114_teratocarcinoma_medulloblastoma_carcinosarcoma_iPS_anaplastic_acute_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr10:103428231..103428251,-p@chr10:103428231..103428251
-
Hg19::chr10:103535882..103535901,-p2@FGF8
Hg19::chr10:103536021..103536028,-p6@FGF8
Hg19::chr10:103536091..103536118,-p5@FGF8
Hg19::chr10:29402307..29402314,-p@chr10:29402307..29402314
-
Hg19::chr10:29543500..29543523,-p@chr10:29543500..29543523
-
Hg19::chr10:36059832..36059842,-p@chr10:36059832..36059842
-
Hg19::chr10:66067384..66067387,-p@chr10:66067384..66067387
-
Hg19::chr10:77873699..77873718,-p@chr10:77873699..77873718
-
Hg19::chr10:8087046..8087057,+p@chr10:8087046..8087057
+
Hg19::chr10:8087174..8087187,+p@chr10:8087174..8087187
+
Hg19::chr10:8087188..8087198,+p@chr10:8087188..8087198
+
Hg19::chr10:8087201..8087204,+p@chr10:8087201..8087204
+
Hg19::chr10:8087205..8087216,+p@chr10:8087205..8087216
+
Hg19::chr10:8087237..8087255,+p@chr10:8087237..8087255
+
Hg19::chr11:15930770..15930778,+p@chr11:15930770..15930778
+
Hg19::chr11:67608319..67608337,+p1@ENST00000528260
Hg19::chr11:71368360..71368362,+p@chr11:71368360..71368362
+
Hg19::chr12:12110721..12110724,-p@chr12:12110721..12110724
-
Hg19::chr12:16940922..16940952,-p@chr12:16940922..16940952
-
Hg19::chr12:1739030..1739033,+p19@WNT5B
Hg19::chr12:1739040..1739046,+p17@WNT5B
Hg19::chr12:1739060..1739078,+p2@WNT5B
Hg19::chr12:1739115..1739120,+p12@WNT5B
Hg19::chr12:1752871..1752874,+p@chr12:1752871..1752874
+
Hg19::chr12:20342245..20342261,+p@chr12:20342245..20342261
+
Hg19::chr12:25783686..25783696,-p6@IFLTD1
Hg19::chr12:25783877..25783885,-p11@IFLTD1
Hg19::chr12:3990487..3990517,-p@chr12:3990487..3990517
-
Hg19::chr12:4378997..4379008,+p@chr12:4378997..4379008
+
Hg19::chr12:4379052..4379063,+p@chr12:4379052..4379063
+
Hg19::chr12:4380403..4380416,+p@chr12:4380403..4380416
+
Hg19::chr12:4381997..4382005,+p@chr12:4381997..4382005
+
Hg19::chr12:4872943..4872966,+p2@GALNT8
Hg19::chr12:5126773..5126779,+p@chr12:5126773..5126779
+
Hg19::chr12:5152939..5152954,+p5@KCNA5
Hg19::chr12:5153018..5153070,+p1@KCNA5
Hg19::chr12:5153088..5153101,+p4@KCNA5
Hg19::chr12:5153106..5153117,+p3@KCNA5
Hg19::chr12:53301815..53301817,-p@chr12:53301815..53301817
-
Hg19::chr12:8472262..8472265,+p@chr12:8472262..8472265
+
Hg19::chr12:8472938..8472944,+p1@ENST00000537764
Hg19::chr13:19495191..19495195,-p@chr13:19495191..19495195
-
Hg19::chr13:54688155..54688160,-p@chr13:54688155..54688160
-
Hg19::chr13:91852841..91852851,-p@chr13:91852841..91852851
-
Hg19::chr14:102713814..102713825,-p27@MOK
Hg19::chr14:102713828..102713844,-p13@MOK
Hg19::chr14:102713851..102713858,-p38@MOK
Hg19::chr14:102713863..102713873,-p29@MOK
Hg19::chr14:102713879..102713893,-p22@MOK
Hg19::chr14:23526715..23526738,-p1@CDH24
Hg19::chr14:23526739..23526766,-p2@CDH24
Hg19::chr14:23526901..23526941,+p@chr14:23526901..23526941
+
Hg19::chr14:23574150..23574161,-p2@uc010aki.1
Hg19::chr14:23574164..23574179,-p3@uc010aki.1
Hg19::chr14:23574186..23574212,-p1@uc010aki.1
Hg19::chr14:23574312..23574323,-p5@uc010aki.1
Hg19::chr14:23574351..23574354,-p4@uc010aki.1
Hg19::chr14:30766237..30766247,-p1@ENST00000508469
Hg19::chr14:74816536..74816574,-p@chr14:74816536..74816574
-
Hg19::chr14:85119696..85119699,+p@chr14:85119696..85119699
+
Hg19::chr14:85404728..85404733,+p@chr14:85404728..85404733
+
Hg19::chr15:90294478..90294480,-p6@MESP1
Hg19::chr15:90294523..90294532,-p9@MESP1
Hg19::chr15:90319557..90319563,+p5@MESP2
Hg19::chr16:19146810..19146823,+p@chr16:19146810..19146823
+
Hg19::chr16:30102547..30102556,-p6@TBX6
Hg19::chr16:51674974..51674989,-p@chr16:51674974..51674989
-
Hg19::chr16:532468..532478,+p13@RAB11FIP3
Hg19::chr16:532503..532516,+p11@RAB11FIP3
Hg19::chr17:60694918..60694923,+p@chr17:60694918..60694923
+
Hg19::chr17:60694974..60694983,+p@chr17:60694974..60694983
+
Hg19::chr17:8788322..8788325,-p@chr17:8788322..8788325
-
Hg19::chr18:57122165..57122171,-p10@CCBE1
Hg19::chr18:57122174..57122181,-p8@CCBE1
Hg19::chr18:57122211..57122214,-p13@CCBE1
Hg19::chr18:57122277..57122323,-p7@CCBE1
Hg19::chr18:57122450..57122454,-p12@CCBE1
Hg19::chr19:6661453..6661459,-p@chr19:6661453..6661459
-
Hg19::chr1:156677222..156677267,-p@chr1:156677222..156677267
-
Hg19::chr1:156722195..156722246,-p6@HDGF
Hg19::chr1:156722252..156722268,-p15@HDGF
Hg19::chr1:156828460..156828465,-p5@INSRR
Hg19::chr1:192536660..192536663,-p1@ENST00000434300
Hg19::chr1:192538307..192538319,-p@chr1:192538307..192538319
-
Hg19::chr1:221509769..221509790,-p1@C1orf140
Hg19::chr1:221539942..221539946,-p@chr1:221539942..221539946
-
Hg19::chr1:221539953..221539960,-p@chr1:221539953..221539960
-
Hg19::chr1:221540010..221540025,-p@chr1:221540010..221540025
-
Hg19::chr1:221540060..221540070,-p@chr1:221540060..221540070
-
Hg19::chr1:231176821..231176832,-p@chr1:231176821..231176832
-
Hg19::chr1:231176858..231176870,-p@chr1:231176858..231176870
-
Hg19::chr1:869192..869225,+p@chr1:869192..869225
+
Hg19::chr20:35960451..35960496,-p@chr20:35960451..35960496
-
Hg19::chr20:35965035..35965042,+p@chr20:35965035..35965042
+
Hg19::chr20:35965049..35965060,+p@chr20:35965049..35965060
+
Hg19::chr20:44395958..44395961,+p@chr20:44395958..44395961
+
Hg19::chr21:37476919..37476932,+p1@ENST00000422473
Hg19::chr2:154449469..154449474,-p6@ENST00000424322
Hg19::chr2:179921760..179921761,-p@chr2:179921760..179921761
-
Hg19::chr2:189039113..189039119,-p@chr2:189039113..189039119
-
Hg19::chr2:202897947..202897953,+p@chr2:202897947..202897953
+
Hg19::chr2:212456729..212456733,-p@chr2:212456729..212456733
-
Hg19::chr2:21277085..21277095,+p@chr2:21277085..21277095
+
Hg19::chr2:21277180..21277193,+p@chr2:21277180..21277193
+
Hg19::chr2:216410860..216410867,+p2@ENST00000417485
Hg19::chr2:216411107..216411114,-p@chr2:216411107..216411114
-
Hg19::chr2:216411710..216411716,+p@chr2:216411710..216411716
+
Hg19::chr2:223616837..223616846,+p@chr2:223616837..223616846
+
Hg19::chr2:31455471..31455477,-p@chr2:31455471..31455477
-
Hg19::chr2:49381628..49381639,-p2@FSHR
Hg19::chr2:49381646..49381667,-p1@FSHR
Hg19::chr2:50059270..50059276,-p@chr2:50059270..50059276
-
Hg19::chr2:85806846..85806848,+p@chr2:85806846..85806848
+
Hg19::chr3:149815776..149815786,+p1@ENST00000489690
Hg19::chr3:163787628..163787675,-p@chr3:163787628..163787675
-
Hg19::chr3:164045034..164045037,-p@chr3:164045034..164045037
-
Hg19::chr3:164049297..164049301,-p@chr3:164049297..164049301
-
Hg19::chr3:164059027..164059038,-p@chr3:164059027..164059038
-
Hg19::chr3:164059048..164059053,-p@chr3:164059048..164059053
-
Hg19::chr3:170541159..170541187,-p@chr3:170541159..170541187
-
Hg19::chr3:175779448..175779449,+p@chr3:175779448..175779449
+
Hg19::chr3:177924489..177924496,-p@chr3:177924489..177924496
-
Hg19::chr3:177924499..177924508,-p@chr3:177924499..177924508
-
Hg19::chr3:177924517..177924527,-p@chr3:177924517..177924527
-
Hg19::chr3:177924555..177924566,-p@chr3:177924555..177924566
-
Hg19::chr3:177924604..177924625,-p@chr3:177924604..177924625
-
Hg19::chr3:189863313..189863317,+p@chr3:189863313..189863317
+
Hg19::chr3:27760311..27760317,+p@chr3:27760311..27760317
+
Hg19::chr3:27761692..27761705,-p4@EOMES
Hg19::chr3:27764190..27764208,-p2@EOMES
Hg19::chr3:72831611..72831631,-p@chr3:72831611..72831631
-
Hg19::chr4:134198028..134198032,+p@chr4:134198028..134198032
+
Hg19::chr4:30718989..30718993,+p@chr4:30718989..30718993
+
Hg19::chr4:53726052..53726074,+p@chr4:53726052..53726074
+
Hg19::chr6:105136637..105136638,-p@chr6:105136637..105136638
-
Hg19::chr6:47624200..47624225,+p1@GPR111
Hg19::chr6:66497726..66497737,-p@chr6:66497726..66497737
-
Hg19::chr7:22743278..22743282,+p@chr7:22743278..22743282
+
Hg19::chr7:33925953..33925962,+p@chr7:33925953..33925962
+
Hg19::chr7:99764987..99765000,-p8@GAL3ST4
Hg19::chr8:35591851..35591852,-p@chr8:35591851..35591852
-
Hg19::chr8:35653945..35653948,-p@chr8:35653945..35653948
-
Hg19::chr8:35701490..35701493,-p@chr8:35701490..35701493
-
Hg19::chr8:8920173..8920180,+p@chr8:8920173..8920180
+
Hg19::chr8:8920182..8920203,+p@chr8:8920182..8920203
+
Hg19::chr9:113361735..113361747,+p1@ENST00000451108
Hg19::chr9:113361757..113361764,+p2@ENST00000451108
Hg19::chr9:129278732..129278753,+p3@ENST00000454034
Hg19::chr9:134424707..134424746,+p@chr9:134424707..134424746
+
Hg19::chr9:140145343..140145351,+p4@C9orf173
Hg19::chr9:20309137..20309163,-p@chr9:20309137..20309163
-
Hg19::chr9:34590839..34590855,-p@chr9:34590839..34590855
-
Hg19::chr9:34590865..34590871,-p@chr9:34590865..34590871
-
Hg19::chr9:71044776..71044789,+p@chr9:71044776..71044789
+
Hg19::chr9:71044863..71044869,+p@chr9:71044863..71044869
+
Hg19::chr9:94711007..94711026,-p6@ROR2
Hg19::chrX:106142727..106142730,-p@chrX:106142727..106142730
-
Hg19::chrX:106146562..106146577,-p1@RIPPLY1
Hg19::chrX:106146585..106146594,-p2@RIPPLY1
Hg19::chrX:136514398..136514433,-p@chrX:136514398..136514433
-
Hg19::chrX:149009969..149009992,+p1@MAGEA8
Hg19::chrX:149009998..149010009,+p2@MAGEA8
Hg19::chrX:26432797..26432802,-p@chrX:26432797..26432802
-


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:0009790embryonic development5.59986875796887e-05
GO:0007275multicellular organismal development0.000321228245153704
GO:0009792embryonic development ending in birth or egg hatching0.00151062087568722
GO:0043009chordate embryonic development0.00151062087568722
GO:0001756somitogenesis0.00227939928363625
GO:0032502developmental process0.00227939928363625
GO:0007369gastrulation0.00362534049682365
GO:0035282segmentation0.00370882200730299
GO:0032501multicellular organismal process0.00431937013855186
GO:0007223Wnt receptor signaling pathway, calcium modulating pathway0.00591953290940296
GO:0007166cell surface receptor linked signal transduction0.00760423583310115
GO:0007219Notch signaling pathway0.0085594792187517
GO:0009952anterior/posterior pattern formation0.00948616385651051
GO:0007154cell communication0.00948616385651051
GO:0030538embryonic genitalia morphogenesis0.00952990698222064
GO:0035112genitalia morphogenesis0.00952990698222064
GO:0007548sex differentiation0.014743204595023
GO:0050698proteoglycan sulfotransferase activity0.014743204595023
GO:0032525somite rostral/caudal axis specification0.014743204595023
GO:0003002regionalization0.014743204595023
GO:0003006reproductive developmental process0.014743204595023
GO:0007165signal transduction0.0166510273928262
GO:0001757somite specification0.0198773798424053
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0201402093437203
GO:0050694galactose 3-O-sulfotransferase activity0.0230723726604471
GO:0001733galactosylceramide sulfotransferase activity0.0230723726604471
GO:0007389pattern specification process0.0230723726604471
GO:0019199transmembrane receptor protein kinase activity0.0233177373540907
GO:0009653anatomical structure morphogenesis0.0245658128113677
GO:0004963follicle-stimulating hormone receptor activity0.0245658128113677
GO:00506563'-phosphoadenosine 5'-phosphosulfate binding0.0245658128113677
GO:0016055Wnt receptor signaling pathway0.0264543460856625
GO:0007379segment specification0.0276846289069627
GO:0005886plasma membrane0.0351665031296109
GO:0048856anatomical structure development0.0387629299511934
GO:0048562embryonic organ morphogenesis0.0411068344774184
GO:0055037recycling endosome0.0411068344774184
GO:0001502cartilage condensation0.0428866821785772
GO:0009948anterior/posterior axis specification0.0428866821785772
GO:0005887integral to plasma membrane0.0440919256064758
GO:0048806genitalia development0.0440919256064758
GO:0031226intrinsic to plasma membrane0.0440919256064758
GO:0005794Golgi apparatus0.044899582208696
GO:0005251delayed rectifier potassium channel activity0.044899582208696
GO:0001824blastocyst development0.0472656664445428
GO:0001707mesoderm formation0.04847326951489
GO:0001708cell fate specification0.04847326951489
GO:0044459plasma membrane part0.0489007058950888
GO:0005509calcium ion binding0.0496262906590614
GO:0008083growth factor activity0.0496262906590614
GO:0048332mesoderm morphogenesis0.0496262906590614
GO:0001704formation of primary germ layer0.0496262906590614



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><br>disease_data<br>

Disease
Ontology termp-valuen
germ cell and embryonal cancer1.80e-1022
germ cell cancer1.80e-1022


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
POU5F1#546048.181443937851360.00155789126614770.00989085750426744



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

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