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Coexpression cluster:C102: Difference between revisions

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|tf_chipseq_enrich=FAM48A#55578;5:30.7225731382979:7.45128886397291e-07:3.29887731099816e-05!GATA2#2624;34:2.30493446245125:4.14202266864013e-06:0.000131445975536344!POU5F1#5460;5:8.92125535776345:0.000273961954058297:0.00292141234632372!REST#5978;35:1.79654789927915:0.000462711121506247:0.0042622232156457!WRNIP1#56897;6:3.50489247923541:0.00789412363568941:0.0324065240512467!ZZZ3#26009;5:6.36737267114982:0.00124200529787877:0.00835246563458857
|tf_chipseq_enrich=FAM48A#55578;5:30.7225731382979:7.45128886397291e-07:3.29887731099816e-05!GATA2#2624;34:2.30493446245125:4.14202266864013e-06:0.000131445975536344!POU5F1#5460;5:8.92125535776345:0.000273961954058297:0.00292141234632372!REST#5978;35:1.79654789927915:0.000462711121506247:0.0042622232156457!WRNIP1#56897;6:3.50489247923541:0.00789412363568941:0.0324065240512467!ZZZ3#26009;5:6.36737267114982:0.00124200529787877:0.00835246563458857
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|tfbs_overrepresentation_for_novel_motifs=0.93788,0.451319,0.117584,1.017,0.688191,0.797839,0.299478,0.156431,0.321633,0.607268,0.345009,0.600426,1.7828,0.169358,0.24885,0.575991,0.031733,0.63244,0.0179993,0.816495,0.011944,0.164637,0.202777,0.0476441,0.566752,0.0198596,0.421151,0.296169,0.577143,0.891193,0.516903,0.122784,0.303914,0.785915,1.94864,0.0400445,0.00564877,0.140977,0.221703,0.0648815,0.258705,0.0936639,0.381834,0.015777,1.04686,0.0451078,0.61601,0.308568,0.433902,0.354723,0.75549,0.125,1.77199,0.198614,0.182107,0.0495925,0.283954,1.52839,1.00954,0.0122657,0.0601302,1.61979,0.148983,0.30646,0.230947,0.0553441,0.0767165,0.272395,0.239618,0.172074,0.192377,0.234552,0.0255332,0.180414,0.0979254,0.45767,0.768127,0.667895,0.412203,0.299115,0.871038,0.0743699,0.0707925,0.0885345,0.326474,0.018724,5.18476,0.0680515,0.00897414,0.34267,0.115042,0.120682,0.482847,0.434092,0.129728,1.0736,1.5017,0.179616,0.168456,0.979849,0.0823977,0.0478231,3.03862,0.207441,0.375652,0.0487984,0.186548,0.0456748,0.098939,0.0370983,1.59698,0.338946,0.67387,0.51641,0.0942771,0.180025,0.0399497,0.00218609,0.1264,0.00594481,0.173491,0.433315,0.446971,0.388897,0.446252,0.0653215,0.00696127,0.0104727,1.21938,0.539521,0.849389,0.395405,0.0623892,0.379115,0.120986,0.09532,0.00608056,0.569657,0.334105,0.721035,0.381998,0.0867243,1.27023,0.347482,0.118971,0.0600173,0.744662,0.580498,1.56087,0.253178,1.26074,0.000578882,0.0293944,0.615992,1.32566,0.189466,0.141202,14.8157,37.3692,0.223523,0.608162,0.265267,0.410446,1.05211,0.0586753,0.0701602,0.512798,0.187207,0.000144408
}}
}}

Revision as of 13:26, 26 November 2012


Full id: C102_neuroblastoma_testicular_pituitary_carcinosarcoma_rectum_acantholytic_iPS



Phase1 CAGE Peaks

Hg19::chr10:127350469..127350475,-p@chr10:127350469..127350475
-
Hg19::chr10:127350497..127350505,-p@chr10:127350497..127350505
-
Hg19::chr11:133821367..133821390,-p@chr11:133821367..133821390
-
Hg19::chr11:68450506..68450518,+p@chr11:68450506..68450518
+
Hg19::chr11:68451165..68451175,+p4@GAL
Hg19::chr11:68451232..68451268,+p5@GAL
Hg19::chr11:68452002..68452019,+p1@GAL
Hg19::chr11:71952309..71952319,-p2@PHOX2A
Hg19::chr11:71955016..71955024,-p7@PHOX2A
Hg19::chr12:122711996..122712008,-p5@DIABLO
Hg19::chr12:122712038..122712049,-p8@DIABLO
Hg19::chr12:49688923..49688936,+p1@PRPH
Hg19::chr14:104690772..104690782,+p@chr14:104690772..104690782
+
Hg19::chr14:104760121..104760131,+p@chr14:104760121..104760131
+
Hg19::chr14:104760198..104760243,+p@chr14:104760198..104760243
+
Hg19::chr14:104760559..104760564,+p@chr14:104760559..104760564
+
Hg19::chr14:104760576..104760581,+p@chr14:104760576..104760581
+
Hg19::chr14:104760588..104760595,+p@chr14:104760588..104760595
+
Hg19::chr14:104760605..104760614,+p@chr14:104760605..104760614
+
Hg19::chr15:74495513..74495544,-p8@STRA6
Hg19::chr16:57980377..57980387,-p@chr16:57980377..57980387
-
Hg19::chr16:57980404..57980415,-p@chr16:57980404..57980415
-
Hg19::chr16:57980416..57980425,-p@chr16:57980416..57980425
-
Hg19::chr16:57980435..57980443,-p@chr16:57980435..57980443
-
Hg19::chr16:57980444..57980463,-p@chr16:57980444..57980463
-
Hg19::chr17:42101631..42101637,-p@chr17:42101631..42101637
-
Hg19::chr17:74540218..74540227,+p12@PRCD
Hg19::chr17:74540293..74540300,+p15@PRCD
Hg19::chr19:4279647..4279659,+p9@SHD
Hg19::chr19:4279661..4279707,+p3@SHD
Hg19::chr19:48876376..48876383,+p@chr19:48876376..48876383
+
Hg19::chr19:48876384..48876391,+p@chr19:48876384..48876391
+
Hg19::chr19:48876418..48876427,+p@chr19:48876418..48876427
+
Hg19::chr19:48876547..48876593,+p@chr19:48876547..48876593
+
Hg19::chr19:48876664..48876672,+p@chr19:48876664..48876672
+
Hg19::chr19:48876673..48876694,+p@chr19:48876673..48876694
+
Hg19::chr19:48876699..48876707,+p@chr19:48876699..48876707
+
Hg19::chr19:48876709..48876718,+p@chr19:48876709..48876718
+
Hg19::chr1:151688655..151688667,-p14@CELF3
Hg19::chr1:151688674..151688683,-p22@CELF3
Hg19::chr1:156626643..156626652,+p14@BCAN
Hg19::chr1:205325698..205325721,-p5@KLHDC8A
Hg19::chr1:207915129..207915176,+p@chr1:207915129..207915176
+
Hg19::chr1:235813246..235813266,-p7@GNG4
Hg19::chr1:245751682..245751686,-p@chr1:245751682..245751686
-
Hg19::chr1:50569575..50569586,+p11@ELAVL4
Hg19::chr21:46690262..46690294,-p7@POFUT2
Hg19::chr22:48962342..48962367,-p@chr22:48962342..48962367
-
Hg19::chr2:16040301..16040302,-p@chr2:16040301..16040302
-
Hg19::chr2:16081362..16081379,-p4@MYCNOS
Hg19::chr2:20691929..20691932,-p@chr2:20691929..20691932
-
Hg19::chr2:20691964..20691969,-p@chr2:20691964..20691969
-
Hg19::chr2:27651478..27651507,+p1@NRBP1
Hg19::chr2:27651519..27651539,+p2@NRBP1
Hg19::chr2:27712583..27712688,-p1@IFT172
Hg19::chr2:27805866..27805879,+p2@ZNF512
Hg19::chr2:27805880..27805967,+p1@ZNF512
Hg19::chr2:27805971..27805981,+p3@ZNF512
Hg19::chr2:27851885..27851930,+p1@GPN1
Hg19::chr2:27884081..27884103,+p@chr2:27884081..27884103
+
Hg19::chr2:27886228..27886239,-p6@SUPT7L
Hg19::chr2:27886258..27886282,-p3@SUPT7L
Hg19::chr2:27886408..27886419,-p4@SUPT7L
Hg19::chr2:27886420..27886431,-p7@SUPT7L
Hg19::chr2:27886432..27886452,-p2@SUPT7L
Hg19::chr2:27886460..27886511,-p1@SUPT7L
Hg19::chr2:27886747..27886783,+p1@SLC4A1AP
Hg19::chr2:27938593..27938615,-p1@ENST00000379677
p1@uc002rll.1
Hg19::chr2:27994567..27994641,+p1@MRPL33
Hg19::chr2:28113583..28113684,+p1@BRE
Hg19::chr2:29439699..29439702,-p@chr2:29439699..29439702
-
Hg19::chr2:29439775..29439786,-p@chr2:29439775..29439786
-
Hg19::chr2:29439892..29439900,-p@chr2:29439892..29439900
-
Hg19::chr2:29439948..29439958,-p@chr2:29439948..29439958
-
Hg19::chr2:29439959..29439970,-p@chr2:29439959..29439970
-
Hg19::chr2:29440063..29440070,-p@chr2:29440063..29440070
-
Hg19::chr2:29440093..29440103,-p@chr2:29440093..29440103
-
Hg19::chr2:29440116..29440123,-p@chr2:29440116..29440123
-
Hg19::chr2:29440133..29440140,-p@chr2:29440133..29440140
-
Hg19::chr2:29440175..29440180,-p@chr2:29440175..29440180
-
Hg19::chr2:29440253..29440264,-p@chr2:29440253..29440264
-
Hg19::chr2:29440474..29440512,-p@chr2:29440474..29440512
-
Hg19::chr2:29450467..29450495,-p@chr2:29450467..29450495
-
Hg19::chr2:29484252..29484254,-p@chr2:29484252..29484254
-
Hg19::chr2:29519868..29519887,-p@chr2:29519868..29519887
-
Hg19::chr2:29576587..29576590,-p@chr2:29576587..29576590
-
Hg19::chr2:29626570..29626576,-p@chr2:29626570..29626576
-
Hg19::chr2:29645795..29645797,+p@chr2:29645795..29645797
+
Hg19::chr2:29650381..29650398,-p@chr2:29650381..29650398
-
Hg19::chr2:29653880..29653881,+p@chr2:29653880..29653881
+
Hg19::chr2:29655619..29655623,+p@chr2:29655619..29655623
+
Hg19::chr2:29658492..29658495,-p@chr2:29658492..29658495
-
Hg19::chr2:29703653..29703657,-p@chr2:29703653..29703657
-
Hg19::chr2:29706034..29706038,-p@chr2:29706034..29706038
-
Hg19::chr2:29727599..29727607,-p@chr2:29727599..29727607
-
Hg19::chr2:29728669..29728672,-p@chr2:29728669..29728672
-
Hg19::chr2:29731597..29731601,-p@chr2:29731597..29731601
-
Hg19::chr2:29747873..29747882,-p@chr2:29747873..29747882
-
Hg19::chr2:29747891..29747899,-p@chr2:29747891..29747899
-
Hg19::chr2:29747901..29747910,-p@chr2:29747901..29747910
-
Hg19::chr2:29747945..29747955,-p@chr2:29747945..29747955
-
Hg19::chr2:29747987..29747993,-p@chr2:29747987..29747993
-
Hg19::chr2:29748214..29748225,-p@chr2:29748214..29748225
-
Hg19::chr2:29796921..29796922,-p@chr2:29796921..29796922
-
Hg19::chr2:29822049..29822052,-p@chr2:29822049..29822052
-
Hg19::chr2:29836771..29836815,-p@chr2:29836771..29836815
-
Hg19::chr2:29863817..29863820,-p@chr2:29863817..29863820
-
Hg19::chr2:29891260..29891294,-p@chr2:29891260..29891294
-
Hg19::chr2:29892736..29892737,-p@chr2:29892736..29892737
-
Hg19::chr2:29894070..29894081,-p@chr2:29894070..29894081
-
Hg19::chr2:29894082..29894092,-p@chr2:29894082..29894092
-
Hg19::chr2:29902123..29902129,-p@chr2:29902123..29902129
-
Hg19::chr2:29902520..29902529,-p@chr2:29902520..29902529
-
Hg19::chr2:29902609..29902616,-p@chr2:29902609..29902616
-
Hg19::chr2:30106068..30106073,-p@chr2:30106068..30106073
-
Hg19::chr2:30106093..30106097,-p@chr2:30106093..30106097
-
Hg19::chr2:30106158..30106162,-p@chr2:30106158..30106162
-
Hg19::chr2:30128567..30128583,-p@chr2:30128567..30128583
-
Hg19::chr2:30130900..30130921,-p@chr2:30130900..30130921
-
Hg19::chr2:30132841..30132846,-p@chr2:30132841..30132846
-
Hg19::chr2:30133779..30133783,-p@chr2:30133779..30133783
-
Hg19::chr2:30142997..30143009,-p@chr2:30142997..30143009
-
Hg19::chr2:30143103..30143109,-p22@ALK
Hg19::chr2:30143599..30143606,-p15@ALK
Hg19::chr2:30143685..30143694,-p11@ALK
Hg19::chr2:30143749..30143756,-p16@ALK
Hg19::chr2:30143760..30143777,-p5@ALK
Hg19::chr2:30143805..30143814,-p6@ALK
Hg19::chr2:30143819..30143830,-p8@ALK
Hg19::chr2:30143841..30143861,-p4@ALK
Hg19::chr2:30144040..30144047,-p19@ALK
Hg19::chr2:30144102..30144111,-p9@ALK
Hg19::chr2:30144125..30144135,-p12@ALK
Hg19::chr2:30144214..30144224,-p14@ALK
Hg19::chr2:30144229..30144240,-p10@ALK
Hg19::chr2:30144445..30144457,-p1@ALK
Hg19::chr2:30144471..30144482,-p2@ALK
Hg19::chr2:30670077..30670125,+p1@LCLAT1
Hg19::chr2:30670127..30670186,+p2@LCLAT1
Hg19::chr2:30670193..30670200,+p5@LCLAT1
Hg19::chr2:30670209..30670220,+p4@LCLAT1
Hg19::chr2:30762138..30762142,+p@chr2:30762138..30762142
+
Hg19::chr2:30863199..30863211,+p@chr2:30863199..30863211
+
Hg19::chr2:30863696..30863716,+p@chr2:30863696..30863716
+
Hg19::chr2:30864128..30864141,+p8@LCLAT1
Hg19::chr2:30864391..30864426,+p6@LCLAT1
Hg19::chr2:30864461..30864472,+p11@LCLAT1
Hg19::chr2:30864778..30864794,+p@chr2:30864778..30864794
+
Hg19::chr2:30864827..30864835,+p@chr2:30864827..30864835
+
Hg19::chr2:30864920..30864931,+p@chr2:30864920..30864931
+
Hg19::chr2:30865194..30865203,+p9@LCLAT1
Hg19::chr2:30865283..30865293,+p3@LCLAT1
Hg19::chr2:30865408..30865436,+p7@LCLAT1
Hg19::chr3:132975822..132975848,-p@chr3:132975822..132975848
-
Hg19::chr3:132975886..132975894,-p1@ENST00000504993
Hg19::chr3:28617116..28617136,+p@chr3:28617116..28617136
+
Hg19::chr3:33998836..33998839,+p@chr3:33998836..33998839
+
Hg19::chr3:97448267..97448299,-p@chr3:97448267..97448299
-
Hg19::chr3:97455832..97455841,-p@chr3:97455832..97455841
-
Hg19::chr3:97483572..97483644,+p1@ARL6
Hg19::chr3:97483652..97483663,+p4@ARL6
Hg19::chr3:97483675..97483686,+p5@ARL6
Hg19::chr4:10057464..10057469,+p@chr4:10057464..10057469
+
Hg19::chr4:175204955..175204970,+p9@CEP44
Hg19::chr4:42400017..42400037,+p4@SHISA3
Hg19::chr4:48485147..48485178,+p6@SLC10A4
Hg19::chr5:16180622..16180633,-p@chr5:16180622..16180633
-
Hg19::chr5:16180836..16180838,-p6@MARCH11
Hg19::chr5:16180906..16180918,-p3@MARCH11
Hg19::chr5:16180927..16180934,-p7@MARCH11
Hg19::chr5:168272120..168272136,-p12@SLIT3
Hg19::chr5:168310338..168310348,-p@chr5:168310338..168310348
-
Hg19::chr5:168310353..168310356,-p@chr5:168310353..168310356
-
Hg19::chr5:168310490..168310493,-p@chr5:168310490..168310493
-
Hg19::chr5:168310509..168310521,-p@chr5:168310509..168310521
-
Hg19::chr5:168310523..168310542,-p@chr5:168310523..168310542
-
Hg19::chr6:119524135..119524144,+p@chr6:119524135..119524144
+
Hg19::chr6:119524165..119524187,+p@chr6:119524165..119524187
+
Hg19::chr6:123318989..123318999,+p@chr6:123318989..123318999
+
Hg19::chr6:159190463..159190467,-p@chr6:159190463..159190467
-
Hg19::chr6:44238930..44238942,+p4@TMEM151B
Hg19::chr6:44355325..44355340,+p4@CDC5L
Hg19::chr6:44355992..44356000,+p@chr6:44355992..44356000
+
Hg19::chr6:44356761..44356774,+p@chr6:44356761..44356774
+
Hg19::chr9:94955376..94955381,+p@chr9:94955376..94955381
+
Hg19::chr9:97372339..97372361,-p@chr9:97372339..97372361
-
Hg19::chrX:133847905..133847915,-p@chrX:133847905..133847915
-
Hg19::chrX:133847967..133848002,-p@chrX:133847967..133848002
-


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

No GOStat results

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
migratory neural crest cell1.77e-1041
neurectodermal cell9.44e-0859
Uber Anatomy
Ontology termp-valuen
sympathetic nervous system3.49e-795
autonomic nervous system3.49e-795
peripheral nervous system9.75e-458
Disease
Ontology termp-valuen
neuroendocrine tumor2.83e-666
neuroectodermal tumor2.00e-4010
germ cell and embryonal cancer3.41e-1922
germ cell cancer3.41e-1922


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
FAM48A#55578530.72257313829797.45128886397291e-073.29887731099816e-05
GATA2#2624342.304934462451254.14202266864013e-060.000131445975536344
POU5F1#546058.921255357763450.0002739619540582970.00292141234632372
REST#5978351.796547899279150.0004627111215062470.0042622232156457
WRNIP1#5689763.504892479235410.007894123635689410.0324065240512467
ZZZ3#2600956.367372671149820.001242005297878770.00835246563458857



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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