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MCL coexpression mm9:200: Difference between revisions

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{{MCL_coexpression_mm9
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oxidoreductase activity;0.0364528008759897;68180,68177!GO:0008903;hydroxypyruvate isomerase activity;0.0364528008759897;68180!GO:0016125;sterol metabolic process;0.0364528008759897;11816,68177!GO:0005159;insulin-like growth factor receptor binding;0.0364528008759897;16000!GO:0047750;cholestenol delta-isomerase activity;0.0364528008759897;68177!GO:0018445;prothoracicotrophic hormone activity;0.0364528008759897;16000!GO:0033143;regulation of steroid hormone receptor signaling pathway;0.0364528008759897;16000!GO:0009653;anatomical structure morphogenesis;0.0364528008759897;11816,16010,16000,18081!GO:0006707;cholesterol catabolic process;0.0364528008759897;11816!GO:0016127;sterol catabolic process;0.0364528008759897;11816!GO:0033344;cholesterol efflux;0.0364528008759897;11816!GO:0008202;steroid metabolic process;0.0364528008759897;11816,68177!GO:0050650;chondroitin sulfate proteoglycan biosynthetic process;0.0364528008759897;16000!GO:0050654;chondroitin sulfate proteoglycan metabolic process;0.0364528008759897;16000!GO:0035239;tube morphogenesis;0.0364528008759897;11816,16000!GO:0016853;isomerase activity;0.0364528008759897;68180,68177!GO:0006706;steroid catabolic process;0.0364528008759897;11816!GO:0065008;regulation of biological quality;0.0364528008759897;11816,16010,16000!GO:0042627;chylomicron;0.0364528008759897;11816!GO:0030104;water homeostasis;0.0364528008759897;16000!GO:0017127;cholesterol transporter activity;0.0364528008759897;11816!GO:0015198;oligopeptide transporter activity;0.0364528008759897;65221!GO:0015248;sterol transporter activity;0.0364528008759897;11816!GO:0015197;peptide transporter activity;0.0364528008759897;65221!GO:0006857;oligopeptide transport;0.0364528008759897;65221!GO:0018987;osmoregulation;0.0364528008759897;16000!GO:0021940;positive regulation of granule cell precursor proliferation;0.0364528008759897;16000!GO:0021936;regulation of granule cell precursor proliferation;0.0364528008759897;16000!GO:0048009;insulin-like growth factor receptor signaling pathway;0.0364528008759897;16000!GO:0035295;tube development;0.0364528008759897;11816,16000!GO:0021534;cell proliferation in hindbrain;0.0364528008759897;16000!GO:0021924;cell proliferation in the external granule layer;0.0364528008759897;16000!GO:0021930;granule cell precursor proliferation;0.0364528008759897;16000!GO:0016861;intramolecular oxidoreductase activity, interconverting aldoses and ketoses;0.0364528008759897;68180!GO:0048878;chemical homeostasis;0.0364528008759897;11816,16000!GO:0031099;regeneration;0.0378566317807004;18081!GO:0042246;tissue regeneration;0.0378566317807004;18081!GO:0006950;response to stress;0.0389874105240323;11816,116891,18081!GO:0030518;steroid hormone receptor signaling pathway;0.0413637874716506;16000!GO:0008034;lipoprotein binding;0.0413637874716506;11816!GO:0042311;vasodilation;0.0424139434841373;11816!GO:0030301;cholesterol transport;0.0424139434841373;11816!GO:0006066;alcohol metabolic process;0.0432302520435786;11816,68177!GO:0015918;sterol transport;0.0432302520435786;11816!GO:0030166;proteoglycan biosynthetic process;0.0432302520435786;16000!GO:0030246;carbohydrate binding;0.0432302520435786;11816,66205!GO:0016863;intramolecular oxidoreductase activity, transposing 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|gostat_on_MCL_coexpression=GO:0016860;intramolecular oxidoreductase activity;0.0364528008759897;68180,68177!GO:0008903;hydroxypyruvate isomerase activity;0.0364528008759897;68180!GO:0016125;sterol metabolic process;0.0364528008759897;11816,68177!GO:0005159;insulin-like growth factor receptor binding;0.0364528008759897;16000!GO:0047750;cholestenol delta-isomerase activity;0.0364528008759897;68177!GO:0018445;prothoracicotrophic hormone activity;0.0364528008759897;16000!GO:0033143;regulation of steroid hormone receptor signaling pathway;0.0364528008759897;16000!GO:0009653;anatomical structure morphogenesis;0.0364528008759897;11816,16010,16000,18081!GO:0006707;cholesterol catabolic process;0.0364528008759897;11816!GO:0016127;sterol catabolic process;0.0364528008759897;11816!GO:0033344;cholesterol efflux;0.0364528008759897;11816!GO:0008202;steroid metabolic process;0.0364528008759897;11816,68177!GO:0050650;chondroitin sulfate proteoglycan biosynthetic process;0.0364528008759897;16000!GO:0050654;chondroitin sulfate proteoglycan metabolic process;0.0364528008759897;16000!GO:0035239;tube morphogenesis;0.0364528008759897;11816,16000!GO:0016853;isomerase activity;0.0364528008759897;68180,68177!GO:0006706;steroid catabolic process;0.0364528008759897;11816!GO:0065008;regulation of biological quality;0.0364528008759897;11816,16010,16000!GO:0042627;chylomicron;0.0364528008759897;11816!GO:0030104;water homeostasis;0.0364528008759897;16000!GO:0017127;cholesterol transporter activity;0.0364528008759897;11816!GO:0015198;oligopeptide transporter activity;0.0364528008759897;65221!GO:0015248;sterol transporter activity;0.0364528008759897;11816!GO:0015197;peptide transporter activity;0.0364528008759897;65221!GO:0006857;oligopeptide transport;0.0364528008759897;65221!GO:0018987;osmoregulation;0.0364528008759897;16000!GO:0021940;positive regulation of granule cell precursor proliferation;0.0364528008759897;16000!GO:0021936;regulation of granule cell precursor proliferation;0.0364528008759897;16000!GO:0048009;insulin-like growth factor receptor signaling pathway;0.0364528008759897;16000!GO:0035295;tube development;0.0364528008759897;11816,16000!GO:0021534;cell proliferation in hindbrain;0.0364528008759897;16000!GO:0021924;cell proliferation in the external granule layer;0.0364528008759897;16000!GO:0021930;granule cell precursor proliferation;0.0364528008759897;16000!GO:0016861;intramolecular oxidoreductase activity, interconverting aldoses and ketoses;0.0364528008759897;68180!GO:0048878;chemical homeostasis;0.0364528008759897;11816,16000!GO:0031099;regeneration;0.0378566317807004;18081!GO:0042246;tissue regeneration;0.0378566317807004;18081!GO:0006950;response to stress;0.0389874105240323;11816,116891,18081!GO:0030518;steroid hormone receptor signaling pathway;0.0413637874716506;16000!GO:0008034;lipoprotein binding;0.0413637874716506;11816!GO:0042311;vasodilation;0.0424139434841373;11816!GO:0030301;cholesterol transport;0.0424139434841373;11816!GO:0006066;alcohol metabolic process;0.0432302520435786;11816,68177!GO:0015918;sterol transport;0.0432302520435786;11816!GO:0030166;proteoglycan biosynthetic process;0.0432302520435786;16000!GO:0030246;carbohydrate binding;0.0432302520435786;11816,66205!GO:0016863;intramolecular oxidoreductase activity, transposing C
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002107!4.59e-13!22;UBERON:0007499!4.59e-13!22;UBERON:0006925!4.59e-13!22;UBERON:0009497!4.59e-13!22;UBERON:0000015!4.59e-13!22;UBERON:0002423!4.59e-13!22;UBERON:0006235!4.59e-13!22;UBERON:0008835!4.59e-13!22;UBERON:0003894!4.59e-13!22;UBERON:0004161!4.59e-13!22;UBERON:0008836!4.59e-13!22;UBERON:0002365!8.46e-13!25;UBERON:0002330!8.46e-13!25;UBERON:0009854!2.69e-12!23;UBERON:0009856!2.69e-12!23;UBERON:0000025!3.73e-11!114;UBERON:0004111!8.60e-11!122;UBERON:0005172!3.54e-09!49;UBERON:0005173!3.54e-09!49;UBERON:0002417!3.54e-09!49;UBERON:0000916!3.54e-09!49;UBERON:0001017!4.30e-09!73;UBERON:0004121!2.27e-08!95;UBERON:0000924!2.27e-08!95;UBERON:0006601!2.27e-08!95;UBERON:0005256!2.38e-08!45;UBERON:0001016!4.12e-08!75;UBERON:0000479!1.63e-07!349;UBERON:0003914!2.46e-07!47;UBERON:0009569!8.55e-07!66
|tfbs_overrepresentation_for_novel_motifs=1.05244,3.54431,0.379048,0.030356,0.0726828,0.136685,5.06168,0.673143,0.0583325,0.302334,0.0474918,0.463399,0.00481301,0.0671124,0.00518677,0,0.160929,1.97811,0.16314,0.274028,0.299601,2.28694,0.873915,0.295417,0.396304,0.0780682,6.27754,0.0397113,0.114423,0.640348,0.601649,1.19162,2.81379,0.109172,7.28567,0.0106026,0.134055,2.83154,0.0438158,1.39028,0.0222582,2.37238,1.0935,0.347032,1.57296,0.0277199,2.43691,0.384626,3.36129,0.0414537,0.460103,1.04482,0.993372,0.32465,0.337879,0.0698741,0.262709,2.76426,1.14199,0.892087,0.210874,2.81646,0.142101,2.02377,1.39648,0.167829,0.446354,0.753619,0.207853,0.620196,0.566162,0.11694,0.0934641,0.363751,1.08041,0.0482891,0.109048,0.111857,0.579573,0.0116415,0.512307,0.171159,0.0931732,0.0987051,0.277331,1.23792,3.28339,0.0733285,0.120031,0.905173,0.504811,0.280902,0.656883,0.0253329,0.00185617,0.0321281,0.0485113,1.91272,0.117671,0.154801,1.16909,0.223826,0.3116,0.460943,0.150653,0.0370932,1.04289,0.0431432,0.0122926,0.011325,0.221124,1.52012,0.310675,0.0491417,0.510816,0.463074,1.99215,0.127722,2.15774,0.855124,0.963393,0.133171,0.0788239,0.359033,0.557481,0.202211,0.503127,0.228022,0.445102,0.176766,0.29905,0.526471,0.420887,0.0753094,0.529327,0.124534,0.0987615,0.0376022,0.487417,1.25998,0.875109,0.450248,1.49266,0.230994,0.882667,0.616815,0.119124,1.22129,1.96308,0.0741073,2.60582,2.31828,1.56613,0.0871025,0.259965,2.68184,0.301851,0.00614531,0.434115,1.08969,0.495459,0.276719,0.202495,1.8243,0.145166,0.0719656,0.0176958,0.0576118,0.591413
}}

Latest revision as of 14:52, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:87322381..87322392,+p20@Igf1
Mm9::chr11:70832735..70832769,-p1@Derl2
Mm9::chr11:98913110..98913132,+p@chr11:98913110..98913132
+
Mm9::chr13:49282854..49282908,+p1@Ninj1
Mm9::chr14:25852233..25852235,-p@chr14:25852233..25852235
-
Mm9::chr14:61979232..61979299,-p1@Ebpl
Mm9::chr19:10917253..10917258,+p4@Slc15a3
Mm9::chr2:60122349..60122358,-p3@Cd302
Mm9::chr4:118032587..118032637,+p1@Hyi
Mm9::chr4:144483030..144483054,+p3@Dhrs3
Mm9::chr4:144483208..144483223,+p4@Dhrs3
Mm9::chr7:135036978..135036995,-p@chr7:135036978..135036995
-
Mm9::chr7:20281617..20281623,+p@chr7:20281617..20281623
+
Mm9::chr7:20281641..20281678,-p@chr7:20281641..20281678
-
Mm9::chr7:20281669..20281686,+p@chr7:20281669..20281686
+
Mm9::chr7:20281713..20281745,+p@chr7:20281713..20281745
+
Mm9::chr7:20281715..20281736,-p@chr7:20281715..20281736
-
Mm9::chr7:20281750..20281788,-p@chr7:20281750..20281788
-
Mm9::chr7:20281778..20281790,+p@chr7:20281778..20281790
+
Mm9::chr7:20281798..20281809,-p@chr7:20281798..20281809
-
Mm9::chr7:20281847..20281854,-p@chr7:20281847..20281854
-
Mm9::chr7:20281878..20281903,+p@chr7:20281878..20281903
+
Mm9::chr7:20281910..20281921,+p@chr7:20281910..20281921
+
Mm9::chr7:20281932..20281988,-p@chr7:20281932..20281988
-
Mm9::chr7:20281997..20282023,-p@chr7:20281997..20282023
-
Mm9::chr7:20282030..20282052,-p@chr7:20282030..20282052
-
Mm9::chr7:20282060..20282097,-p@chr7:20282060..20282097
-
Mm9::chr7:20282155..20282173,-p@chr7:20282155..20282173
-
Mm9::chr7:20282217..20282244,-p@chr7:20282217..20282244
-
Mm9::chr7:20282223..20282246,+p@chr7:20282223..20282246
+
Mm9::chr7:20282263..20282292,-p@chr7:20282263..20282292
-
Mm9::chr7:20282292..20282308,+p@chr7:20282292..20282308
+
Mm9::chr7:20282296..20282318,-p@chr7:20282296..20282318
-
Mm9::chr7:20282325..20282339,+p@chr7:20282325..20282339
+
Mm9::chr7:20282330..20282384,-p@chr7:20282330..20282384
-
Mm9::chr7:20282360..20282433,+p@chr7:20282360..20282433
+
Mm9::chr7:20282392..20282404,-p@chr7:20282392..20282404
-
Mm9::chr7:20282410..20282460,-p@chr7:20282410..20282460
-
Mm9::chr7:20282814..20282847,+p@chr7:20282814..20282847
+
Mm9::chr7:20282853..20282871,-p@chr7:20282853..20282871
-
Mm9::chr7:20282883..20282937,-p@chr7:20282883..20282937
-
Mm9::chr7:20282943..20282956,-p@chr7:20282943..20282956
-
Mm9::chr7:20282961..20282984,-p@chr7:20282961..20282984
-
Mm9::chr7:20282989..20283002,-p@chr7:20282989..20283002
-
Mm9::chr7:20283555..20283610,-p2@Apoe
Mm9::chr7:20284394..20284412,-p1@Apoe
Mm9::chr7:56653449..56653462,+p@chr7:56653449..56653462
+


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:0016860intramolecular oxidoreductase activity0.0364528008759897
GO:0008903hydroxypyruvate isomerase activity0.0364528008759897
GO:0016125sterol metabolic process0.0364528008759897
GO:0005159insulin-like growth factor receptor binding0.0364528008759897
GO:0047750cholestenol delta-isomerase activity0.0364528008759897
GO:0018445prothoracicotrophic hormone activity0.0364528008759897
GO:0033143regulation of steroid hormone receptor signaling pathway0.0364528008759897
GO:0009653anatomical structure morphogenesis0.0364528008759897
GO:0006707cholesterol catabolic process0.0364528008759897
GO:0016127sterol catabolic process0.0364528008759897
GO:0033344cholesterol efflux0.0364528008759897
GO:0008202steroid metabolic process0.0364528008759897
GO:0050650chondroitin sulfate proteoglycan biosynthetic process0.0364528008759897
GO:0050654chondroitin sulfate proteoglycan metabolic process0.0364528008759897
GO:0035239tube morphogenesis0.0364528008759897
GO:0016853isomerase activity0.0364528008759897
GO:0006706steroid catabolic process0.0364528008759897
GO:0065008regulation of biological quality0.0364528008759897
GO:0042627chylomicron0.0364528008759897
GO:0030104water homeostasis0.0364528008759897
GO:0017127cholesterol transporter activity0.0364528008759897
GO:0015198oligopeptide transporter activity0.0364528008759897
GO:0015248sterol transporter activity0.0364528008759897
GO:0015197peptide transporter activity0.0364528008759897
GO:0006857oligopeptide transport0.0364528008759897
GO:0018987osmoregulation0.0364528008759897
GO:0021940positive regulation of granule cell precursor proliferation0.0364528008759897
GO:0021936regulation of granule cell precursor proliferation0.0364528008759897
GO:0048009insulin-like growth factor receptor signaling pathway0.0364528008759897
GO:0035295tube development0.0364528008759897
GO:0021534cell proliferation in hindbrain0.0364528008759897
GO:0021924cell proliferation in the external granule layer0.0364528008759897
GO:0021930granule cell precursor proliferation0.0364528008759897
GO:0016861intramolecular oxidoreductase activity, interconverting aldoses and ketoses0.0364528008759897
GO:0048878chemical homeostasis0.0364528008759897
GO:0031099regeneration0.0378566317807004
GO:0042246tissue regeneration0.0378566317807004
GO:0006950response to stress0.0389874105240323
GO:0030518steroid hormone receptor signaling pathway0.0413637874716506
GO:0008034lipoprotein binding0.0413637874716506
GO:0042311vasodilation0.0424139434841373
GO:0030301cholesterol transport0.0424139434841373
GO:0006066alcohol metabolic process0.0432302520435786
GO:0015918sterol transport0.0432302520435786
GO:0030166proteoglycan biosynthetic process0.0432302520435786
GO:0030246carbohydrate binding0.0432302520435786
GO:0016863intramolecular oxidoreductase activity, transposing C



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
liver4.59e-1322
epithelial sac4.59e-1322
digestive gland4.59e-1322
epithelium of foregut-midgut junction4.59e-1322
anatomical boundary4.59e-1322
hepatobiliary system4.59e-1322
foregut-midgut junction4.59e-1322
hepatic diverticulum4.59e-1322
liver primordium4.59e-1322
septum transversum4.59e-1322
liver bud4.59e-1322
exocrine gland8.46e-1325
exocrine system8.46e-1325
digestive tract diverticulum2.69e-1223
sac2.69e-1223
tube3.73e-11114
anatomical conduit8.60e-11122
abdomen element3.54e-0949
abdominal segment element3.54e-0949
abdominal segment of trunk3.54e-0949
abdomen3.54e-0949
central nervous system4.30e-0973
ectoderm-derived structure2.27e-0895
ectoderm2.27e-0895
presumptive ectoderm2.27e-0895
trunk mesenchyme2.38e-0845
nervous system4.12e-0875
tissue1.63e-07349
epithelial tube2.46e-0747
subdivision of trunk8.55e-0766


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)
MA0003.10.0778476
MA0004.10.0304736
MA0006.11.06357
MA0007.10.0269583
MA0009.10.241801
MA0014.10.0013401
MA0017.10.00704285
MA0019.10.130554
MA0024.10.212626
MA0025.11.0712
MA0027.11.75175
MA0028.10.0311147
MA0029.10.198677
MA0030.10.202852
MA0031.10.533273
MA0038.10.268681
MA0040.10.250394
MA0041.10.904638
MA0042.10.334683
MA0043.10.310854
MA0046.10.266754
MA0048.14.06197
MA0050.10.040802
MA0051.10.0817759
MA0052.10.255985
MA0055.10.839737
MA0056.10
MA0057.10.0058574
MA0058.10.012403
MA0059.11.61144
MA0060.10.267728
MA0061.10.0136212
MA0063.10
MA0066.11.92091
MA0067.10.509729
MA0068.10.0408783
MA0069.10.256221
MA0070.10.249498
MA0071.10.361715
MA0072.10.243673
MA0073.10.000178708
MA0074.10.472995
MA0076.10.00898052
MA0077.10.229013
MA0078.10.096354
MA0081.10.655586
MA0083.10.310264
MA0084.10.803542
MA0087.10.7636
MA0088.10.0484674
MA0089.10
MA0090.10.744633
MA0091.11.77109
MA0092.10.0228919
MA0093.10.00633797
MA0095.10
MA0098.10
MA0100.10.0558545
MA0101.10.072051
MA0103.11.29557
MA0105.10.050803
MA0106.10.328653
MA0107.10.0393423
MA0108.20.142919
MA0109.10
MA0111.10.265314
MA0113.10.29406
MA0114.10.0443644
MA0115.10.312936
MA0116.10.527003
MA0117.10.289199
MA0119.10.0156385
MA0122.10.303728
MA0124.10.464833
MA0125.10.404137
MA0130.10
MA0131.10.128156
MA0132.10
MA0133.10
MA0135.10.338295
MA0136.11.32345
MA0139.14.18795
MA0140.10.450401
MA0141.10.010293
MA0142.10.171883
MA0143.10.0944901
MA0144.11.0454
MA0145.10.00187004
MA0146.12.5891
MA0147.10.240132
MA0148.10.589204
MA0149.10.0164376
MA0062.20.191828
MA0035.20.057452
MA0039.22.32997e-06
MA0138.20.12401
MA0002.23.32564
MA0137.20.738366
MA0104.20.00628566
MA0047.20.0777193
MA0112.20.250857
MA0065.20.00189931
MA0150.10.507854
MA0151.10
MA0152.10.0777635
MA0153.10.351062
MA0154.10.00221483
MA0155.10.0232317
MA0156.10.262286
MA0157.10.465757
MA0158.10
MA0159.10.431713
MA0160.10.03537
MA0161.10
MA0162.10.0255464
MA0163.10.0810138
MA0164.10.0674435
MA0080.20.932426
MA0018.20.0712081
MA0099.20.120763
MA0079.23.15008e-11
MA0102.20.852517
MA0258.10.010524
MA0259.10.00221835
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:200&oldid=3072199"