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Coexpression cluster:C114: Difference between revisions

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{{Coexpression_clusters
{
|full_id=C114_teratocarcinoma_medulloblastoma_carcinosarcoma_iPS_anaplastic_acute_neuroblastoma
 

Latest revision as of 10:34, 17 September 2013


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)
MA0003.10.000871686
MA0004.10.027215
MA0006.10.00203387
MA0007.11.04039
MA0009.11.28744
MA0014.10.153415
MA0017.10.416056
MA0019.11.4166
MA0024.10.0678697
MA0025.10.246672
MA0027.11.23274
MA0028.10.0349457
MA0029.10.199303
MA0030.10.186425
MA0031.10.685069
MA0038.10.8666
MA0040.10.0808574
MA0041.10.336182
MA0042.11.0795
MA0043.10.0324176
MA0046.10.12354
MA0048.10.394596
MA0050.10.15856
MA0051.10.6268
MA0052.10.0184598
MA0055.10.186637
MA0056.10
MA0057.13.6789
MA0058.10.0244882
MA0059.10.0238699
MA0060.10.00238065
MA0061.10.0474021
MA0063.10
MA0066.10.304579
MA0067.10.151402
MA0068.11.20015
MA0069.10.120866
MA0070.10.113288
MA0071.10.126901
MA0072.10.498928
MA0073.10.0282567
MA0074.10.291499
MA0076.10.00193797
MA0077.10.105341
MA0078.10.120634
MA0081.10.0239472
MA0083.10.583497
MA0084.10.264265
MA0087.10.108727
MA0088.10.0165868
MA0089.10
MA0090.10.724456
MA0091.10.188008
MA0092.12.5706
MA0093.10.0058044
MA0095.10
MA0098.10
MA0100.10.0547508
MA0101.10.132459
MA0103.10.300151
MA0105.10.224435
MA0106.10.0287631
MA0107.10.157211
MA0108.21.6843
MA0109.10
MA0111.10.242044
MA0113.10.666078
MA0114.10.349562
MA0115.11.21013
MA0116.10.0297197
MA0117.10.159975
MA0119.10.0634839
MA0122.10.181523
MA0124.10.31706
MA0125.11.28924
MA0130.10
MA0131.10.0190788
MA0132.10
MA0133.10
MA0135.10.993412
MA0136.10.0187412
MA0139.10.136259
MA0140.10.480464
MA0141.10.0808498
MA0142.11.15752
MA0143.11.1897
MA0144.11.92053
MA0145.10.499563
MA0146.10.0104048
MA0147.10.00187786
MA0148.10.504118
MA0149.10.303609
MA0062.20.00469455
MA0035.21.11344
MA0039.20.0202345
MA0138.20.00252816
MA0002.20.338552
MA0137.20.340033
MA0104.20.00230219
MA0047.20.773138
MA0112.20.405082
MA0065.21.02138
MA0150.10.0721314
MA0151.10
MA0152.10.224827
MA0153.10.466073
MA0154.11.40492
MA0155.10.228946
MA0156.10.000395811
MA0157.10.504474
MA0158.10
MA0159.10.086114
MA0160.10.273868
MA0161.10
MA0162.10.00485124
MA0163.10.728597
MA0164.10.190593
MA0080.20.0131263
MA0018.20.151407
MA0099.20.506336
MA0079.21.9919
MA0102.20.289716
MA0258.10.00563171
MA0259.10.00588262
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

(#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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