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MCL coexpression mm9:107: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000010!1.41e-14!11;UBERON:0002410!2.40e-12!9;UBERON:0004121!1.21e-07!95;UBERON:0000924!1.21e-07!95;UBERON:0006601!1.21e-07!95;UBERON:0002240!2.81e-07!6;UBERON:0005174!2.81e-07!6;UBERON:0001137!2.81e-07!6
|ontology_enrichment_uberon=UBERON:0000010!1.41e-14!11;UBERON:0002410!2.40e-12!9;UBERON:0004121!1.21e-07!95;UBERON:0000924!1.21e-07!95;UBERON:0006601!1.21e-07!95;UBERON:0002240!2.81e-07!6;UBERON:0005174!2.81e-07!6;UBERON:0001137!2.81e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.503159,1.10691,0.170078,0.0521699,0.243808,0.754187,0.670444,0.154402,0.258453,0.0845913,0.197336,0.417103,0.067055,0.485629,0.132904,0,0.112347,0.218496,1.49099,0.652015,0.0103872,3.05708,0.162501,0.00533194,0.430839,0.200799,0.193715,0.274396,0.294836,0.332939,0.137944,0.42794,0.416425,1.07169,0.916322,0.00745044,0.0202342,0.612579,1.17106,0.00194867,0.230775,0.403137,0.940392,0.0817943,1.32389,0.181633,0.573383,0.48038,0.593637,0.204396,0.10084,0.114914,0.564937,0.104494,0.112375,0.172897,0.227764,0.229953,0.487636,0.0766032,0.698828,0.256077,0.0669819,0.720434,0.540298,0.0291236,0.183634,0.428549,0.687035,0.848564,0.0362177,0.548306,0.056327,1.30401,0.436712,0.356744,0.407439,0.542482,0.160443,0.293493,0.33484,0.864451,0.25375,0.0336901,0.0780168,0.313163,0.707082,3.55975,0.06803,0.563177,0.226121,0.0799154,0.449926,1.73807,0.120016,0.371898,3.00862,0.791202,0.574084,2.17954e-07,0.371591,1.14836,0.0969166,0.101221,0.100547,0.144344,0.142745,0.301004,0.0664651,0.185732,0.326029,0.663019,0.0629492,1.02123,0.230622,0.920173,0.675115,0.502671,1.18099,0.957123,0.813927,0.0814654,0.363519,0.159638,0.266365,0.163505,0.701465,0.438232,0.182752,1.27161,0.625522,0.102806,0.165943,0.0877862,0.685031,10.6902,0.537619,0.071851,0.611375,0.895958,0.53599,0.186385,0.39095,0.0550024,0.239001,0.591277,0.874313,0.858873,0.381368,0.0320136,0.350533,0.0243245,0.342607,0.0329205,0.0290719,0.144703,0.242629,0.478216,0.21841,0.0116388,0.219161,0.267721,0.37337,0.203714,0.445582,0.0817301,0.796543,0.250255,1.82928
}}
}}

Revision as of 17:48, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128241409..128241430,-p5@Tmem198b
Mm9::chr10:38684998..38685007,+p9@Lama4
Mm9::chr10:8482017..8482057,-p@chr10:8482017..8482057
-
Mm9::chr10:8482067..8482081,-p@chr10:8482067..8482081
-
Mm9::chr10:85484738..85484760,+p5@Fbxo7
Mm9::chr10:85484763..85484772,+p8@Fbxo7
Mm9::chr10:85495802..85495813,+p11@Fbxo7
Mm9::chr11:113795301..113795315,+p@chr11:113795301..113795315
+
Mm9::chr11:113927488..113927502,-p2@Sdk2
Mm9::chr11:35357986..35357997,+p6@Slit3
Mm9::chr11:35358006..35358022,+p5@Slit3
Mm9::chr11:5872449..5872475,-p@chr11:5872449..5872475
-
Mm9::chr11:5872687..5872711,-p@chr11:5872687..5872711
-
Mm9::chr12:88020400..88020411,+p@chr12:88020400..88020411
+
Mm9::chr13:115629493..115629504,+p@chr13:115629493..115629504
+
Mm9::chr13:26078079..26078090,-p@chr13:26078079..26078090
-
Mm9::chr14:104243452..104243455,-p15@Ednrb
Mm9::chr15:78986963..78986976,-p@chr15:78986963..78986976
-
Mm9::chr15:78994288..78994299,-p@chr15:78994288..78994299
-
Mm9::chr15:78994907..78994926,-p1@Sox10
Mm9::chr15:90848413..90848436,-p@chr15:90848413..90848436
-
Mm9::chr16:35853680..35853695,-p@chr16:35853680..35853695
-
Mm9::chr17:64660640..64660669,-p@chr17:64660640..64660669
-
Mm9::chr17:72942954..72942965,-p@chr17:72942954..72942965
-
Mm9::chr17:72953973..72953985,-p1@Alk
Mm9::chr18:32109348..32109364,-p4@Gpr17
Mm9::chr18:32109368..32109396,-p2@Gpr17
Mm9::chr18:32109449..32109468,-p3@Gpr17
Mm9::chr18:32109476..32109489,-p5@Gpr17
Mm9::chr18:32109524..32109538,-p6@Gpr17
Mm9::chr18:43367276..43367332,+p1@LOC100047004
p1@Stk32a
Mm9::chr18:43367333..43367354,+p2@LOC100047004
p2@Stk32a
Mm9::chr18:69752864..69752875,+p25@Tcf4
Mm9::chr18:69752912..69752928,+p9@Tcf4
Mm9::chr19:10347420..10347423,-p@chr19:10347420..10347423
-
Mm9::chr19:10379344..10379355,-p2@Dagla
Mm9::chr19:40457062..40457090,-p@chr19:40457062..40457090
-
Mm9::chr19:40457288..40457305,-p3@Sorbs1
Mm9::chr19:40457348..40457363,-p2@Sorbs1
Mm9::chr19:47538896..47538940,-p3@Sh3pxd2a
Mm9::chr19:57082677..57082713,-p1@Afap1l2
Mm9::chr1:112818931..112818935,-p@chr1:112818931..112818935
-
Mm9::chr1:112856387..112856393,-p@chr1:112856387..112856393
-
Mm9::chr1:138130615..138130628,-p@chr1:138130615..138130628
-
Mm9::chr1:138130630..138130657,-p2@5730559C18Rik
Mm9::chr1:138130690..138130711,-p4@5730559C18Rik
Mm9::chr1:168931103..168931148,+p2@Fam78b
Mm9::chr1:65358027..65358031,+p1@Pth2r
Mm9::chr1:94648758..94648763,+p@chr1:94648758..94648763
+
Mm9::chr2:125549260..125549273,-p4@Shc4
Mm9::chr2:125549393..125549427,-p1@Shc4
Mm9::chr2:125549443..125549459,-p6@Shc4
Mm9::chr2:18238569..18238603,-p@chr2:18238569..18238603
-
Mm9::chr2:58420009..58420022,-p6@Acvr1
Mm9::chr2:83564233..83564263,+p2@Itgav
Mm9::chr3:34095664..34095678,+p1@ENSMUST00000172560
Mm9::chr3:34095699..34095712,+p2@ENSMUST00000172560
Mm9::chr3:34095844..34095855,+p1@ENSMUST00000174785
Mm9::chr3:34101597..34101601,+p@chr3:34101597..34101601
+
Mm9::chr3:97841362..97841366,+p@chr3:97841362..97841366
+
Mm9::chr4:129727954..129727978,+p@chr4:129727954..129727978
+
Mm9::chr4:129727985..129727993,+p@chr4:129727985..129727993
+
Mm9::chr4:129732334..129732345,+p8@Col16a1
Mm9::chr4:129733417..129733462,+p@chr4:129733417..129733462
+
Mm9::chr4:144482577..144482586,+p16@Dhrs3
Mm9::chr4:144590339..144590345,+p@chr4:144590339..144590345
+
Mm9::chr4:98789176..98789188,-p@chr4:98789176..98789188
-
Mm9::chr4:99321776..99321807,-p1@ENSMUST00000136525
Mm9::chr4:99322678..99322679,-p@chr4:99322678..99322679
-
Mm9::chr4:99322689..99322723,-p@chr4:99322689..99322723
-
Mm9::chr4:99322726..99322731,-p@chr4:99322726..99322731
-
Mm9::chr4:99322820..99322845,+p1@Foxd3
Mm9::chr4:99322855..99322867,+p2@Foxd3
Mm9::chr4:99323046..99323073,+p3@Foxd3
Mm9::chr5:151992717..151992728,-p6@Stard13
Mm9::chr5:151992729..151992794,-p1@Stard13
Mm9::chr5:152036343..152036366,-p4@Stard13
Mm9::chr5:152036393..152036426,-p2@Stard13
Mm9::chr5:152036622..152036641,-p3@Stard13
Mm9::chr5:67490447..67490458,-p7@Phox2b
Mm9::chr5:67490474..67490494,-p2@Phox2b
Mm9::chr6:103524593..103524596,+p@chr6:103524593..103524596
+
Mm9::chr6:126711807..126711820,+p@chr6:126711807..126711820
+
Mm9::chr7:121889040..121889050,+p10@Insc
Mm9::chr7:121889188..121889197,+p9@Insc
Mm9::chr7:121889199..121889232,+p1@Insc
Mm9::chr7:121889421..121889445,+p2@Insc
Mm9::chr7:121889453..121889464,+p7@Insc
Mm9::chr7:121897212..121897227,+p12@Insc
Mm9::chr7:26033443..26033484,-p@chr7:26033443..26033484
-
Mm9::chr7:31838093..31838109,-p6@Fxyd1
Mm9::chr7:31838142..31838171,-p4@Fxyd1
Mm9::chr7:31844379..31844401,+p6@Lgi4
Mm9::chr7:31844407..31844429,+p2@Lgi4
Mm9::chr7:31844442..31844458,+p4@Lgi4
Mm9::chr7:31844566..31844654,+p1@Lgi4
Mm9::chr7:31844661..31844676,+p8@Lgi4
Mm9::chr7:31844692..31844718,+p5@Lgi4
Mm9::chr7:31845082..31845100,+p10@Lgi4
Mm9::chr7:38151719..38151721,-p@chr7:38151719..38151721
-
Mm9::chr7:38348671..38348675,-p@chr7:38348671..38348675
-
Mm9::chr7:38554436..38554440,-p@chr7:38554436..38554440
-
Mm9::chr7:38554684..38554696,-p10@Zfp536
Mm9::chr7:38555776..38555815,-p@chr7:38555776..38555815
-
Mm9::chr7:38557861..38557890,+p@chr7:38557861..38557890
+
Mm9::chr7:38557887..38557910,-p5@Zfp536
Mm9::chr7:38559002..38559009,-p15@Zfp536
Mm9::chr7:38559019..38559026,-p21@Zfp536
Mm9::chr7:56531440..56531447,+p@chr7:56531440..56531447
+
Mm9::chr8:59810908..59810928,+p1@ENSMUST00000132988
Mm9::chr8:59811222..59811252,+p@chr8:59811222..59811252
+
Mm9::chr8:95350156..95350173,+p@chr8:95350156..95350173
+
Mm9::chr9:20777404..20777418,+p@chr9:20777404..20777418
+


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

GO IDGO nameFDR corrected p-value
GO:0030318melanocyte differentiation0.0245230399177696
GO:0050931pigment cell differentiation0.0245230399177696
GO:0007275multicellular organismal development0.0245230399177696
GO:0001755neural crest cell migration0.0245230399177696
GO:0007422peripheral nervous system development0.0245230399177696
GO:0001701in utero embryonic development0.0245230399177696
GO:0048066pigmentation during development0.0245230399177696
GO:0014032neural crest cell development0.0245230399177696
GO:0014033neural crest cell differentiation0.0245230399177696
GO:0022610biological adhesion0.0245230399177696
GO:0007155cell adhesion0.0245230399177696
GO:0048731system development0.0245230399177696
GO:0014031mesenchymal cell development0.0245230399177696
GO:0048762mesenchymal cell differentiation0.0245230399177696
GO:0048869cellular developmental process0.0245230399177696
GO:0030154cell differentiation0.0245230399177696
GO:0001829trophectodermal cell differentiation0.0245230399177696
GO:0050431transforming growth factor beta binding0.0245230399177696
GO:0001600endothelin-B receptor activity0.0245230399177696
GO:0030971receptor tyrosine kinase binding0.0245230399177696
GO:0007497posterior midgut development0.0245230399177696
GO:0048646anatomical structure formation0.0343096837245323
GO:0005667transcription factor complex0.0343096837245323
GO:0032502developmental process0.0343096837245323
GO:0001568blood vessel development0.0343096837245323
GO:0001944vasculature development0.0343096837245323
GO:0016361activin receptor activity, type I0.0343096837245323
GO:0017002activin receptor activity0.0343096837245323
GO:0004962endothelin receptor activity0.0343096837245323
GO:0007494midgut development0.0343096837245323
GO:0048856anatomical structure development0.0345956572711971
GO:0009790embryonic development0.0345956572711971
GO:0005201extracellular matrix structural constituent0.0345956572711971
GO:0048468cell development0.0354617629518457
GO:0043009chordate embryonic development0.0355391392346548
GO:0009792embryonic development ending in birth or egg hatching0.0358877002660932
GO:0005025transforming growth factor beta receptor activity, type I0.039562073686022
GO:0048484enteric nervous system development0.039562073686022
GO:0043149stress fiber formation0.039562073686022
GO:0019199transmembrane receptor protein kinase activity0.0419181546907758
GO:0048469cell maturation0.0419966051958706
GO:0044451nucleoplasm part0.0461431632330263
GO:0060037pharyngeal system development0.0463915369030656
GO:0043277apoptotic cell clearance0.0463915369030656
GO:0007167enzyme linked receptor protein signaling pathway0.0463915369030656
GO:0051179localization0.0476151749188097
GO:0016477cell migration0.0476151749188097
GO:0005654nucleoplasm0.0476151749188097
GO:0048041focal adhesion formation0.0494938416044267
GO:0005606laminin-1 complex0.0494938416044267
GO:0001825blastocyst formation0.0494938416044267
GO:0021700developmental maturation0.0494938416044267
GO:0044420extracellular matrix part0.0495976462553279



Relative expression of the co-expression cluster over median <br>Analyst:




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><br>

Cell Type
Ontology termp-valuen
autonomic neuron2.40e-129
ectodermal cell1.00e-0944
neurectodermal cell1.00e-0944
neural cell5.73e-0943
neuron1.46e-0833
neuronal stem cell1.46e-0833
neuroblast1.46e-0833
electrically signaling cell1.46e-0833
non-terminally differentiated cell4.95e-0749

Uber Anatomy
Ontology termp-valuen
peripheral nervous system1.41e-1411
autonomic nervous system2.40e-129
ectoderm-derived structure1.21e-0795
ectoderm1.21e-0795
presumptive ectoderm1.21e-0795
spinal cord2.81e-076
dorsal region element2.81e-076
dorsum2.81e-076


TFBS overrepresentation<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}}}

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