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MCL coexpression mm9:666: Difference between revisions

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{{MCL_coexpression_mm9
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E activity;0.00304059606640004;12876!GO:0030070;insulin processing;0.00304059606640004;12876!GO:0016486;peptide hormone processing;0.0141847842229041;12876!GO:0004182;carboxypeptidase A activity;0.0364292092115519;12876!GO:0004181;metallocarboxypeptidase activity;0.0364292092115519;12876!GO:0004180;carboxypeptidase activity;0.0424727922720623;12876!GO:0008235;metalloexopeptidase activity;0.0476395688666937;12876!GO:0016485;protein 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0147246734237327,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0856562580541553,0,0.0771606661507038,0,0,0,0,0,0,0,0,0.0800187930544913,0.18440492317299,0.129243247362761,0,0,0,0,0,0.113809739605487,0.141204588184303,0.0818436986734574,0.103807782330171,0,0.268800900821362,0.442001048825766,0.0501827898833331,0.0761636383140293,0,0.813300310962814,0.58082481854121,0.71158592685949,0.144779277929812,0.21495333609522,0.182104477852721,0.578848857132785,0.327466262382121,0.402774059390807,0.486061930039393,0.630890265140597,0.241944181742968,0,0,0,0,0,0,0,0,0.0570741246689917,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0825867363219064,0,0,0,0,0.113803446464706,0.163608743054207,0.0514050548005424,0.129576677486723,0.09889124026805,0.210415946511272,0.122046233034924,0,0,0,0,0,0,0,0,0,0.0151042838227393,0.0388988969149198,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0828894264954325,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0646640766951323,0.0914641362800683,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.136990127740213,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.194445471641185,0.376754964798171,0.434359137099159,0.307735388878776,0.226621173458704,0.399810008829701,0.371076178555103,0.278900414858752,0.372806586713801,0.407098602473158,0,0,0,0,0,0,0.0871588832444397,0,0,0,0,0,0.0388749848471105,0,0,0,0,0,0,0,0,0,0.0853789765816907,0,0.0390607415003592,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0004183;carboxypeptidase E activity;0.00304059606640004;12876!GO:0030070;insulin processing;0.00304059606640004;12876!GO:0016486;peptide hormone processing;0.0141847842229041;12876!GO:0004182;carboxypeptidase A activity;0.0364292092115519;12876!GO:0004181;metallocarboxypeptidase activity;0.0364292092115519;12876!GO:0004180;carboxypeptidase activity;0.0424727922720623;12876!GO:0008235;metalloexopeptidase activity;0.0476395688666937;12876!GO:0016485;protein processing;0.0499913764335937;12876!
|ontology_enrichment_celltype=CL:0000117!2.89e-30!23;CL:0000337!2.89e-30!23;CL:0002319!9.68e-20!43;CL:0000540!3.01e-19!33;CL:0000047!3.01e-19!33;CL:0000031!3.01e-19!33;CL:0000404!3.01e-19!33;CL:0000221!3.93e-19!44;CL:0000133!3.93e-19!44;CL:0000055!1.81e-16!49;CL:0000393!2.25e-15!39;CL:0000211!2.25e-15!39;CL:0002321!1.60e-09!70;CL:0002610!4.47e-07!3
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.15e-44!54;UBERON:0001017!3.37e-42!73;UBERON:0002020!4.16e-41!34;UBERON:0001016!9.01e-41!75;UBERON:0001049!1.24e-40!52;UBERON:0005068!1.24e-40!52;UBERON:0006241!1.24e-40!52;UBERON:0007135!1.24e-40!52;UBERON:0002346!1.19e-34!64;UBERON:0003075!1.19e-34!64;UBERON:0007284!1.19e-34!64;UBERON:0004121!9.07e-33!95;UBERON:0000924!9.07e-33!95;UBERON:0006601!9.07e-33!95;UBERON:0003528!2.79e-32!29;UBERON:0002791!2.79e-32!29;UBERON:0001893!2.79e-32!29;UBERON:0002616!6.33e-31!46;UBERON:0000955!4.44e-30!47;UBERON:0006238!4.44e-30!47;UBERON:0010371!4.32e-29!73;UBERON:0003080!9.20e-28!40;UBERON:0002780!1.83e-26!39;UBERON:0001890!1.83e-26!39;UBERON:0006240!1.83e-26!39;UBERON:0003056!1.76e-24!49;UBERON:0010314!6.14e-21!92;UBERON:0000956!3.48e-20!21;UBERON:0001869!3.48e-20!21;UBERON:0000203!3.48e-20!21;UBERON:0002021!9.78e-18!10;UBERON:0000411!9.78e-18!10;UBERON:0001950!9.78e-18!10;UBERON:0002619!1.40e-17!17;UBERON:0002420!2.16e-13!8;UBERON:0007245!2.16e-13!8;UBERON:0010009!2.16e-13!8;UBERON:0010011!2.16e-13!8;UBERON:0000454!2.16e-13!8;UBERON:0000025!4.28e-13!114;UBERON:0003076!6.60e-13!12;UBERON:0003057!6.60e-13!12;UBERON:0004111!1.34e-11!122;UBERON:0002240!2.54e-11!6;UBERON:0005174!2.54e-11!6;UBERON:0001137!2.54e-11!6;UBERON:0001948!5.68e-10!5;UBERON:0002315!5.68e-10!5;UBERON:0000064!6.43e-09!99;UBERON:0011216!8.66e-09!194;UBERON:0000369!2.36e-08!5;UBERON:0002435!2.36e-08!5;UBERON:0000204!2.36e-08!5;UBERON:0010082!2.36e-08!5;UBERON:0002950!6.49e-08!4;UBERON:0001891!6.49e-08!4;UBERON:0009616!6.49e-08!4;UBERON:0010286!6.49e-08!4;UBERON:0004684!4.47e-07!3;UBERON:0002275!4.47e-07!3
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.0513547,0.269904,0.878892,0.52369,0.342839,0.425757,0.345089,0.112618,0.081847,0.385334,0.414631,0.345518,0.437133,0.555819,0,0.619876,0.508485,0.096222,0.171249,1.24695,0.117252,0.436294,0.520732,0.276437,0.4628,0.304017,0.361771,0.213277,0.231659,0.349031,0.717576,0.168723,0.270473,0.19035,0.308746,0.161521,0.411296,0.445168,0.123934,0.51597,0.353696,0.770976,0.559697,0.195622,0.319944,0.543674,0.376103,0.660525,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.223087,0.40287,0.60268,0.441884,0.698157,0.496904,0.383763,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.355763,0.126035,0.905636,0.0810502,0.54852,0.270351,0.532872,0.681539,0.242107,0.724739,0.636582,0.495545,1.13,0.792744,0.0439644,0.0525502,0.231893,1.3522,1.51408,1.07554,0.797601,0.730003,0.535058,0.141946,1.30853,0.694736,0.732731,0.543917,0.197581,0.161581,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.286453,0.840348,0.243062,0.390066,1.0825,0.512539,0.0135638,0.333247,0.621127,0.931584,0.910937,0.572279,1.17341,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,0.540802,0.821997,0.323373,0.976125,0.456508,1.10385,3.19188,0.300001,0.934673,1.05527,1.88134,1.48237,1.01139,1.19763,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,0.178088,0.0664621,0.0240729,0.857198,0.415832,0.455644,0.93735,0.488969,0.199652,0.790184,0.299755,1.06466,0.791909,0.685546,0.776587,0.593295,0.448733,0.484323,0.413167,0.276798
}}

Latest revision as of 15:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:85023868..85023879,+p@chr12:85023868..85023879
+
Mm9::chr2:164317532..164317534,+p@chr2:164317532..164317534
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Mm9::chr2:180764007..180764024,-p@chr2:180764007..180764024
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Mm9::chr2:31139664..31139677,+p@chr2:31139664..31139677
+
Mm9::chr2:90730407..90730420,+p@chr2:90730407..90730420
+
Mm9::chr3:88548978..88548990,-p@chr3:88548978..88548990
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Mm9::chr5:136386450..136386468,-p@chr5:136386450..136386468
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Mm9::chr7:148613898..148613907,-p@chr7:148613898..148613907
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Mm9::chr8:67071668..67071696,-p@chr8:67071668..67071696
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Mm9::chr8:67087900..67087910,-p@chr8:67087900..67087910
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Mm9::chrX:7218219..7218235,+p@chrX:7218219..7218235
+


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:0004183carboxypeptidase E activity0.00304059606640004
GO:0030070insulin processing0.00304059606640004
GO:0016486peptide hormone processing0.0141847842229041
GO:0004182carboxypeptidase A activity0.0364292092115519
GO:0004181metallocarboxypeptidase activity0.0364292092115519
GO:0004180carboxypeptidase activity0.0424727922720623
GO:0008235metalloexopeptidase activity0.0476395688666937
GO:0016485protein processing0.0499913764335937



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>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.15e-4454
central nervous system3.37e-4273
gray matter4.16e-4134
nervous system9.01e-4175
neural tube1.24e-4052
neural rod1.24e-4052
future spinal cord1.24e-4052
neural keel1.24e-4052
neurectoderm1.19e-3464
neural plate1.19e-3464
presumptive neural plate1.19e-3464
ectoderm-derived structure9.07e-3395
ectoderm9.07e-3395
presumptive ectoderm9.07e-3395
brain grey matter2.79e-3229
regional part of telencephalon2.79e-3229
telencephalon2.79e-3229
regional part of brain6.33e-3146
brain4.44e-3047
future brain4.44e-3047
ecto-epithelium4.32e-2973
anterior neural tube9.20e-2840
regional part of forebrain1.83e-2639
forebrain1.83e-2639
future forebrain1.83e-2639
pre-chordal neural plate1.76e-2449
structure with developmental contribution from neural crest6.14e-2192
cerebral cortex3.48e-2021
cerebral hemisphere3.48e-2021
pallium3.48e-2021
occipital lobe9.78e-1810
visual cortex9.78e-1810
neocortex9.78e-1810
regional part of cerebral cortex1.40e-1717
basal ganglion2.16e-138
nuclear complex of neuraxis2.16e-138
aggregate regional part of brain2.16e-138
collection of basal ganglia2.16e-138
cerebral subcortex2.16e-138
tube4.28e-13114
posterior neural tube6.60e-1312
chordal neural plate6.60e-1312
anatomical conduit1.34e-11122
spinal cord2.54e-116
dorsal region element2.54e-116
dorsum2.54e-116
regional part of spinal cord5.68e-105
gray matter of spinal cord5.68e-105
organ part6.43e-0999
organ system subdivision8.66e-09194
corpus striatum2.36e-085
striatum2.36e-085
ventral part of telencephalon2.36e-085
future corpus striatum2.36e-085
regional part of midbrain6.49e-084
midbrain6.49e-084
presumptive midbrain6.49e-084
midbrain neural tube6.49e-084
raphe nuclei4.47e-073
reticular formation4.47e-073


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)
MA0003.10.0832519
MA0004.10.330313
MA0006.10.186435
MA0007.10.316976
MA0009.10.743257
MA0014.10.00333639
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.10.679737
MA0030.10.686088
MA0031.11.56948
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.10.054097
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.0098576
MA0056.10
MA0057.10.406124
MA0058.10.246908
MA0059.10.257372
MA0060.10.12537
MA0061.10.451296
MA0063.10
MA0066.11.1475
MA0067.11.08124
MA0068.10.0500842
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.12.58254e-05
MA0074.10.419185
MA0076.10.223625
MA0077.10.724865
MA0078.11.25398
MA0081.10.277253
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.0293443
MA0089.10
MA0090.10.299987
MA0091.10.906056
MA0092.10.300264
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.619698
MA0105.10.556739
MA0106.10.509454
MA0107.10.211681
MA0108.20.589413
MA0109.10
MA0111.10.839864
MA0113.10.482899
MA0114.10.446898
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.10.733279
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.10.338099
MA0140.11.05203
MA0141.10.658164
MA0142.10.63775
MA0143.10.49828
MA0144.10.452699
MA0145.10.0329586
MA0146.10.0276106
MA0147.10.157258
MA0148.10.344843
MA0149.10.269772
MA0062.20.0791588
MA0035.20.412747
MA0039.20.0156442
MA0138.20.555696
MA0002.20.343346
MA0137.21.21712
MA0104.20.11535
MA0047.20.46201
MA0112.21.29895
MA0065.20.133827
MA0150.10.849777
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.434137
MA0155.10.154271
MA0156.10.222905
MA0157.11.47574
MA0158.10
MA0159.10.165031
MA0160.10.347545
MA0161.10
MA0162.10.0355033
MA0163.10.00559554
MA0164.11.11611
MA0080.20.212408
MA0018.20.446948
MA0099.20.549696
MA0079.20.000447684
MA0102.21.45844
MA0258.11.34967
MA0259.10.14914
MA0442.10
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