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MCL coexpression mm9:977: Difference between revisions

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{{MCL_coexpression_mm9
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receptor protein tyrosine kinase signaling pathway;0.0078468093272825;18596,16948!GO:0007167;enzyme linked receptor protein signaling pathway;0.0104734073596937;18596,16948!GO:0048251;elastic fiber assembly;0.010846937592383;16948!GO:0004720;protein-lysine 6-oxidase activity;0.0162690691681711;16948!GO:0005021;vascular endothelial growth factor receptor activity;0.0216897149435109;18596!GO:0030199;collagen fibril organization;0.0247841703113544;16948!GO:0016641;oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor;0.0247841703113544;16948!GO:0016638;oxidoreductase activity, acting on the CH-NH2 group of donors;0.0271047146771474;16948!GO:0050730;regulation of peptidyl-tyrosine phosphorylation;0.0306023212323308;18596!GO:0005581;collagen;0.0306023212323308;16948!GO:0001932;regulation of protein amino acid phosphorylation;0.0306023212323308;18596!GO:0033238;regulation of amine metabolic process;0.0306023212323308;18596!GO:0006521;regulation of amino acid metabolic process;0.0306023212323308;18596!GO:0005507;copper ion binding;0.0306023212323308;16948!GO:0018212;peptidyl-tyrosine modification;0.0306023212323308;18596!GO:0042325;regulation of phosphorylation;0.0306023212323308;18596!GO:0018108;peptidyl-tyrosine phosphorylation;0.0306023212323308;18596!GO:0051174;regulation of phosphorus metabolic process;0.0306023212323308;18596!GO:0019220;regulation of phosphate metabolic process;0.0306023212323308;18596!GO:0030198;extracellular matrix organization and biogenesis;0.0306023212323308;16948!GO:0004714;transmembrane receptor protein tyrosine kinase activity;0.0306023212323308;18596!GO:0030324;lung development;0.0306023212323308;16948!GO:0030323;respiratory tube development;0.0306023212323308;16948!GO:0019199;transmembrane receptor protein kinase activity;0.0329294981744104;18596!GO:0044420;extracellular matrix part;0.0387029986977406;16948!GO:0018193;peptidyl-amino acid modification;0.0387029986977406;18596!GO:0043062;extracellular structure organization and biogenesis;0.0396675041538477;16948!GO:0005615;extracellular space;0.0411665423765647;18596,16948!GO:0044421;extracellular region 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|gostat_on_MCL_coexpression=GO:0007169;transmembrane receptor protein tyrosine kinase signaling pathway;0.0078468093272825;18596,16948!GO:0007167;enzyme linked receptor protein signaling pathway;0.0104734073596937;18596,16948!GO:0048251;elastic fiber assembly;0.010846937592383;16948!GO:0004720;protein-lysine 6-oxidase activity;0.0162690691681711;16948!GO:0005021;vascular endothelial growth factor receptor activity;0.0216897149435109;18596!GO:0030199;collagen fibril organization;0.0247841703113544;16948!GO:0016641;oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor;0.0247841703113544;16948!GO:0016638;oxidoreductase activity, acting on the CH-NH2 group of donors;0.0271047146771474;16948!GO:0050730;regulation of peptidyl-tyrosine phosphorylation;0.0306023212323308;18596!GO:0005581;collagen;0.0306023212323308;16948!GO:0001932;regulation of protein amino acid phosphorylation;0.0306023212323308;18596!GO:0033238;regulation of amine metabolic process;0.0306023212323308;18596!GO:0006521;regulation of amino acid metabolic process;0.0306023212323308;18596!GO:0005507;copper ion binding;0.0306023212323308;16948!GO:0018212;peptidyl-tyrosine modification;0.0306023212323308;18596!GO:0042325;regulation of phosphorylation;0.0306023212323308;18596!GO:0018108;peptidyl-tyrosine phosphorylation;0.0306023212323308;18596!GO:0051174;regulation of phosphorus metabolic process;0.0306023212323308;18596!GO:0019220;regulation of phosphate metabolic process;0.0306023212323308;18596!GO:0030198;extracellular matrix organization and biogenesis;0.0306023212323308;16948!GO:0004714;transmembrane receptor protein tyrosine kinase activity;0.0306023212323308;18596!GO:0030324;lung development;0.0306023212323308;16948!GO:0030323;respiratory tube development;0.0306023212323308;16948!GO:0019199;transmembrane receptor protein kinase activity;0.0329294981744104;18596!GO:0044420;extracellular matrix part;0.0387029986977406;16948!GO:0018193;peptidyl-amino acid modification;0.0387029986977406;18596!GO:0043062;extracellular structure organization and biogenesis;0.0396675041538477;16948!GO:0005615;extracellular space;0.0411665423765647;18596,16948!GO:0044421;extracellular region part;0.04465246371108;18596,16948!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,1.13872,0.538088,0.515265,1.02512,0.687027,0.494602,0.526159,0.173454,1.35627,0.756943,0,0.742571,0.252772,0.160384,0.29826,0.332107,0.485665,0.549359,0.258745,0.374936,0.577606,0.909128,1.18318,0.303071,0.757024,1.15331,0.843667,0.250677,0.136998,0.757987,4.29115,0.242032,0.522578,0.221921,2.41256,0.256422,0.460258,0.450632,0.27776,0.403938,0.423266,0.662995,1.21655,0.687215,0.305876,0.725127,0.604356,1.2032,0.985264,1.00271,0.557354,0.314394,0.513517,0.877107,0.555328,1.92541,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.527912,0.0665967,2.35974,0.140213,0.409836,0.136938,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.501608,0.920903,0.108172,0.540827,0.757533,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.510015,0.859272,0.663249,0.332938,0.242106,3.25899,0.967837,0.725721,0.724668,0.459825,0.784351,2.09671,0.340849,2.41655,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.333069,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,2.45994,0.854131,1.70776,2.03014,0.666107,1.9792,0.403515,0.261837,0.381863,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,1.94732,0.524587,0.558175
}}

Latest revision as of 16:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr18:52689249..52689272,-p1@Lox
Mm9::chr18:52689284..52689297,-p3@Lox
Mm9::chr18:52689310..52689327,-p2@Lox
Mm9::chr18:52689346..52689363,-p4@Lox
Mm9::chr18:52689457..52689483,-p6@Lox
Mm9::chr18:61204893..61204902,+p6@Pdgfrb
Mm9::chr2:30297583..30297598,+p@chr2:30297583..30297598
+
Mm9::chr6:113640950..113640970,+p@chr6:113640950..113640970
+


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:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0078468093272825
GO:0007167enzyme linked receptor protein signaling pathway0.0104734073596937
GO:0048251elastic fiber assembly0.010846937592383
GO:0004720protein-lysine 6-oxidase activity0.0162690691681711
GO:0005021vascular endothelial growth factor receptor activity0.0216897149435109
GO:0030199collagen fibril organization0.0247841703113544
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.0247841703113544
GO:0016638oxidoreductase activity, acting on the CH-NH2 group of donors0.0271047146771474
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.0306023212323308
GO:0005581collagen0.0306023212323308
GO:0001932regulation of protein amino acid phosphorylation0.0306023212323308
GO:0033238regulation of amine metabolic process0.0306023212323308
GO:0006521regulation of amino acid metabolic process0.0306023212323308
GO:0005507copper ion binding0.0306023212323308
GO:0018212peptidyl-tyrosine modification0.0306023212323308
GO:0042325regulation of phosphorylation0.0306023212323308
GO:0018108peptidyl-tyrosine phosphorylation0.0306023212323308
GO:0051174regulation of phosphorus metabolic process0.0306023212323308
GO:0019220regulation of phosphate metabolic process0.0306023212323308
GO:0030198extracellular matrix organization and biogenesis0.0306023212323308
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0306023212323308
GO:0030324lung development0.0306023212323308
GO:0030323respiratory tube development0.0306023212323308
GO:0019199transmembrane receptor protein kinase activity0.0329294981744104
GO:0044420extracellular matrix part0.0387029986977406
GO:0018193peptidyl-amino acid modification0.0387029986977406
GO:0043062extracellular structure organization and biogenesis0.0396675041538477
GO:0005615extracellular space0.0411665423765647
GO:0044421extracellular region part0.04465246371108



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><br><br>


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)
MA0003.10.016751
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.18.85639
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.282934
MA0056.10
MA0057.15.88339
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.11.61305
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.19.15579
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.15.11227
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.13.50866
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.0701568
MA0146.10.0771944
MA0147.10.236889
MA0148.11.14345
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.22.04793
MA0138.20.675599
MA0002.20.988033
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.90045
MA0065.20.528619
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.10.978338
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.11.276
MA0160.10.453546
MA0161.10
MA0162.10.0211019
MA0163.10.669601
MA0164.11.35808
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.217.893
MA0102.21.59466
MA0258.10.60477
MA0259.10.227035
MA0442.10
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