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MCL coexpression mm9:469: Difference between revisions

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{{MCL_coexpression_mm9
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metabolic process;0.0124910973538596;11816,235293!GO:0050046;lathosterol oxidase activity;0.0124910973538596;235293!GO:0046996;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with NADH or NADPH as one donor, and the other dehydrogenated;0.0124910973538596;235293!GO:0008202;steroid metabolic process;0.014831918205804;11816,235293!GO:0006707;cholesterol catabolic process;0.0214080307195393;11816!GO:0016127;sterol catabolic process;0.0214080307195393;11816!GO:0033344;cholesterol efflux;0.0214080307195393;11816!GO:0006066;alcohol metabolic process;0.0218486435308822;11816,235293!GO:0006706;steroid catabolic process;0.0218486435308822;11816!GO:0042627;chylomicron;0.0218486435308822;11816!GO:0017127;cholesterol transporter activity;0.0218486435308822;11816!GO:0015248;sterol transporter activity;0.0218486435308822;11816!GO:0008034;lipoprotein binding;0.0318104378325636;11816!GO:0042311;vasodilation;0.0318104378325636;11816!GO:0030301;cholesterol transport;0.0318104378325636;11816!GO:0004683;calmodulin-dependent protein kinase activity;0.0318104378325636;227541!GO:0015918;sterol transport;0.0318104378325636;11816!GO:0042632;cholesterol homeostasis;0.0318104378325636;11816!GO:0055088;lipid homeostasis;0.0318104378325636;11816!GO:0055092;sterol homeostasis;0.0318104378325636;11816!GO:0044255;cellular lipid metabolic process;0.0361080724977768;11816,235293!GO:0007163;establishment and/or maintenance of cell polarity;0.0408027456076468;93742!GO:0005913;cell-cell adherens junction;0.0415734311569283;93742!GO:0006629;lipid metabolic process;0.0415734311569283;11816,235293!GO:0044242;cellular lipid catabolic process;0.0417010481539018;11816!GO:0016126;sterol biosynthetic process;0.0417010481539018;235293!GO:0003018;vascular process in circulatory system;0.0438151927516389;11816!GO:0035150;regulation of tube size;0.0438151927516389;11816!GO:0050880;regulation of blood vessel 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.639243382371494,0,0.343480447297274,0.659175921957184,0.44593214273782,0.130103680446068,0,0,0,0,0,0,0,0,0,0,0.195003616524743,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.44384412465388,0,0,0,0,0,0,0.054906696497384,0.0652566657696677,0.10536076625968,0,0.189507698950794,0.164276239518825,0.644242189426794,1.04353409324531,0.83182642302666,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.017244733229267,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0016125;sterol metabolic process;0.0124910973538596;11816,235293!GO:0050046;lathosterol oxidase activity;0.0124910973538596;235293!GO:0046996;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with NADH or NADPH as one donor, and the other dehydrogenated;0.0124910973538596;235293!GO:0008202;steroid metabolic process;0.014831918205804;11816,235293!GO:0006707;cholesterol catabolic process;0.0214080307195393;11816!GO:0016127;sterol catabolic process;0.0214080307195393;11816!GO:0033344;cholesterol efflux;0.0214080307195393;11816!GO:0006066;alcohol metabolic process;0.0218486435308822;11816,235293!GO:0006706;steroid catabolic process;0.0218486435308822;11816!GO:0042627;chylomicron;0.0218486435308822;11816!GO:0017127;cholesterol transporter activity;0.0218486435308822;11816!GO:0015248;sterol transporter activity;0.0218486435308822;11816!GO:0008034;lipoprotein binding;0.0318104378325636;11816!GO:0042311;vasodilation;0.0318104378325636;11816!GO:0030301;cholesterol transport;0.0318104378325636;11816!GO:0004683;calmodulin-dependent protein kinase activity;0.0318104378325636;227541!GO:0015918;sterol transport;0.0318104378325636;11816!GO:0042632;cholesterol homeostasis;0.0318104378325636;11816!GO:0055088;lipid homeostasis;0.0318104378325636;11816!GO:0055092;sterol homeostasis;0.0318104378325636;11816!GO:0044255;cellular lipid metabolic process;0.0361080724977768;11816,235293!GO:0007163;establishment and/or maintenance of cell polarity;0.0408027456076468;93742!GO:0005913;cell-cell adherens junction;0.0415734311569283;93742!GO:0006629;lipid metabolic process;0.0415734311569283;11816,235293!GO:0044242;cellular lipid catabolic process;0.0417010481539018;11816!GO:0016126;sterol biosynthetic process;0.0417010481539018;235293!GO:0003018;vascular process in circulatory system;0.0438151927516389;11816!GO:0035150;regulation of tube size;0.0438151927516389;11816!GO:0050880;regulation of blood vessel size;0.0438151927516389;11816!GO:0005819;spindle;0.0473220262945199;93742!
|ontology_enrichment_celltype=CL:0000181!6.97e-11!5;CL:0000417!6.97e-11!5;CL:0000668!6.97e-11!5;CL:0000412!6.97e-11!5;CL:0000182!6.97e-11!5;CL:0000057!4.68e-07!1;CL:0000632!4.68e-07!1
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002107!2.66e-41!22;UBERON:0007499!2.66e-41!22;UBERON:0006925!2.66e-41!22;UBERON:0009497!2.66e-41!22;UBERON:0000015!2.66e-41!22;UBERON:0002423!2.66e-41!22;UBERON:0006235!2.66e-41!22;UBERON:0008835!2.66e-41!22;UBERON:0003894!2.66e-41!22;UBERON:0004161!2.66e-41!22;UBERON:0008836!2.66e-41!22;UBERON:0009854!1.92e-39!23;UBERON:0009856!1.92e-39!23;UBERON:0002365!3.60e-36!25;UBERON:0002330!3.60e-36!25;UBERON:0005256!2.12e-19!45;UBERON:0003914!1.67e-18!47;UBERON:0005172!1.11e-17!49;UBERON:0005173!1.11e-17!49;UBERON:0002417!1.11e-17!49;UBERON:0000916!1.11e-17!49;UBERON:0003929!1.43e-15!55;UBERON:0002368!3.92e-14!60;UBERON:0003104!7.13e-14!61;UBERON:0009142!7.13e-14!61;UBERON:0002530!6.49e-13!65;UBERON:0000490!1.08e-12!66;UBERON:0009569!1.08e-12!66;UBERON:0005911!4.59e-12!69;UBERON:0001041!6.64e-12!80;UBERON:0000949!1.73e-11!72;UBERON:0000466!2.58e-10!79;UBERON:0005177!2.58e-10!79;UBERON:0002100!7.81e-09!90;UBERON:0004921!8.73e-08!114;UBERON:0001007!1.29e-07!116;UBERON:0001555!1.29e-07!116;UBERON:0007026!1.29e-07!116;UBERON:0004119!1.87e-07!118;UBERON:0000925!1.87e-07!118;UBERON:0006595!1.87e-07!118
}}

Latest revision as of 15:21, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr18:65382340..65382345,-p@chr18:65382340..65382345
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Mm9::chr2:5597108..5597111,-p11@Camk1d
Mm9::chr3:121517222..121517245,-p@chr3:121517222..121517245
-
Mm9::chr3:138037110..138037127,+p1@Adh6-ps1
Mm9::chr4:41691973..41691986,-p9@Sigmar1
Mm9::chr6:121087499..121087514,+p@chr6:121087499..121087514
+
Mm9::chr7:15021789..15021806,-p@chr7:15021789..15021806
-
Mm9::chr7:20283537..20283548,-p@chr7:20283537..20283548
-
Mm9::chr8:129971569..129971578,+p16@Pard3
Mm9::chr8:88125923..88125936,+p@chr8:88125923..88125936
+
Mm9::chr8:88125941..88125950,+p@chr8:88125941..88125950
+
Mm9::chr8:88125965..88125972,+p@chr8:88125965..88125972
+
Mm9::chr8:89139298..89139300,+p@chr8:89139298..89139300
+
Mm9::chr9:42070219..42070224,-p@chr9:42070219..42070224
-
Mm9::chr9:42072287..42072302,-p2@Sc5d
Mm9::chr9:62193253..62193260,+p@chr9:62193253..62193260
+


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:0016125sterol metabolic process0.0124910973538596
GO:0050046lathosterol oxidase activity0.0124910973538596
GO:0046996oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with NADH or NADPH as one donor, and the other dehydrogenated0.0124910973538596
GO:0008202steroid metabolic process0.014831918205804
GO:0006707cholesterol catabolic process0.0214080307195393
GO:0016127sterol catabolic process0.0214080307195393
GO:0033344cholesterol efflux0.0214080307195393
GO:0006066alcohol metabolic process0.0218486435308822
GO:0006706steroid catabolic process0.0218486435308822
GO:0042627chylomicron0.0218486435308822
GO:0017127cholesterol transporter activity0.0218486435308822
GO:0015248sterol transporter activity0.0218486435308822
GO:0008034lipoprotein binding0.0318104378325636
GO:0042311vasodilation0.0318104378325636
GO:0030301cholesterol transport0.0318104378325636
GO:0004683calmodulin-dependent protein kinase activity0.0318104378325636
GO:0015918sterol transport0.0318104378325636
GO:0042632cholesterol homeostasis0.0318104378325636
GO:0055088lipid homeostasis0.0318104378325636
GO:0055092sterol homeostasis0.0318104378325636
GO:0044255cellular lipid metabolic process0.0361080724977768
GO:0007163establishment and/or maintenance of cell polarity0.0408027456076468
GO:0005913cell-cell adherens junction0.0415734311569283
GO:0006629lipid metabolic process0.0415734311569283
GO:0044242cellular lipid catabolic process0.0417010481539018
GO:0016126sterol biosynthetic process0.0417010481539018
GO:0003018vascular process in circulatory system0.0438151927516389
GO:0035150regulation of tube size0.0438151927516389
GO:0050880regulation of blood vessel size0.0438151927516389
GO:0005819spindle0.0473220262945199



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
metabolising cell6.97e-115
endopolyploid cell6.97e-115
parenchymal cell6.97e-115
polyploid cell6.97e-115
hepatocyte6.97e-115
fibroblast4.68e-071
hepatic stellate cell4.68e-071

Uber Anatomy
Ontology termp-valuen
liver2.66e-4122
epithelial sac2.66e-4122
digestive gland2.66e-4122
epithelium of foregut-midgut junction2.66e-4122
anatomical boundary2.66e-4122
hepatobiliary system2.66e-4122
foregut-midgut junction2.66e-4122
hepatic diverticulum2.66e-4122
liver primordium2.66e-4122
septum transversum2.66e-4122
liver bud2.66e-4122
digestive tract diverticulum1.92e-3923
sac1.92e-3923
exocrine gland3.60e-3625
exocrine system3.60e-3625
trunk mesenchyme2.12e-1945
epithelial tube1.67e-1847
abdomen element1.11e-1749
abdominal segment element1.11e-1749
abdominal segment of trunk1.11e-1749
abdomen1.11e-1749
gut epithelium1.43e-1555
endocrine gland3.92e-1460
mesenchyme7.13e-1461
entire embryonic mesenchyme7.13e-1461
gland6.49e-1365
unilaminar epithelium1.08e-1266
subdivision of trunk1.08e-1266
endo-epithelium4.59e-1269
foregut6.64e-1280
endocrine system1.73e-1172
immaterial anatomical entity2.58e-1079
trunk region element2.58e-1079
trunk7.81e-0990
subdivision of digestive tract8.73e-08114
digestive system1.29e-07116
digestive tract1.29e-07116
primitive gut1.29e-07116
endoderm-derived structure1.87e-07118
endoderm1.87e-07118
presumptive endoderm1.87e-07118


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)
MA0003.10.00105703
MA0004.10.221835
MA0006.10.105852
MA0007.10.210531
MA0009.11.45988
MA0014.10.0783947
MA0017.10.774877
MA0019.10.434009
MA0024.10.558971
MA0025.10.819843
MA0027.12.21717
MA0028.10.112137
MA0029.10.53905
MA0030.11.34526
MA0031.11.27635
MA0038.10.897243
MA0040.10.611015
MA0041.10.166538
MA0042.10.15744
MA0043.10.689898
MA0046.10.632833
MA0048.10.219669
MA0050.10.251816
MA0051.10.345658
MA0052.10.618515
MA0055.10.0395234
MA0056.10
MA0057.10.0166073
MA0058.10.464825
MA0059.10.48573
MA0060.11.26961
MA0061.10.0774738
MA0063.10
MA0066.10.328887
MA0067.10.92691
MA0068.10.0176199
MA0069.10.618831
MA0070.10.609808
MA0071.11.29438
MA0072.11.46522
MA0073.15.26061e-07
MA0074.10.299171
MA0076.10.134359
MA0077.11.42301
MA0078.10.976277
MA0081.10.177433
MA0083.10.68915
MA0084.11.24749
MA0087.10.648637
MA0088.10.67791
MA0089.10
MA0090.10.570974
MA0091.10.231874
MA0092.10.196497
MA0093.10.374263
MA0095.10
MA0098.10
MA0100.10.289731
MA0101.10.167439
MA0103.10.404646
MA0105.10.128193
MA0106.10.380511
MA0107.10.125067
MA0108.20.454274
MA0109.10
MA0111.10.595954
MA0113.10.356344
MA0114.11.41638
MA0115.10.692537
MA0116.14.48654
MA0117.10.662171
MA0119.10.502046
MA0122.10.680832
MA0124.10.875485
MA0125.10.804312
MA0130.10
MA0131.10.43
MA0132.10
MA0133.10
MA0135.10.724328
MA0136.10.315568
MA0139.10.406429
MA0140.10.788302
MA0141.11.38795
MA0142.10.499475
MA0143.11.72227
MA0144.10.566612
MA0145.10.00977282
MA0146.10.00479338
MA0147.10.0844713
MA0148.10.660829
MA0149.10.171305
MA0062.20.0332891
MA0035.20.293466
MA0039.20.0724026
MA0138.20.423003
MA0002.20.413675
MA0137.20.852405
MA0104.20.0556953
MA0047.20.895806
MA0112.20.0491092
MA0065.21.79736
MA0150.11.13926
MA0151.10
MA0152.10.337555
MA0153.10.740107
MA0154.10.215016
MA0155.10.0605786
MA0156.10.133796
MA0157.11.18655
MA0158.10
MA0159.10.0900717
MA0160.11.92394
MA0161.10
MA0162.10.138028
MA0163.10.000767531
MA0164.10.315868
MA0080.20.396013
MA0018.20.323932
MA0099.20.417463
MA0079.25.98769e-06
MA0102.21.29919
MA0258.11.34452
MA0259.10.0787033
MA0442.10
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