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MCL coexpression mm9:331: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0.00268807136610733,0.104058634336105,0.125930758668059,0.0677829478188817,0.0710918926542609,1.19334500170986,1.02462566532129,0.0159949728887046,0.00238355079539863,0,0,0,0.00532843399084987,0.00763057558443913,0.00520274619145633,0.0390317607936011,0,0.116729685674643,0.118327974104713,0.12949097173818,0.0258943615634069,0.0157564706642868,0.0151191293499499,0.724990704687569,0.715022915444072,0.290303567558098,0.479316610733703,0.470674196952599,0.121480328532491,0.159873904345373,0.314306540361309,0,0,0,0.544526648606597,0.413952012610508,0.415605580300839,0,0,0,0.014072970156151,0,0,0.00620963879248839,0.00334069834331448,0.0163504569282015,0,0.00654873566263546,0.012754575686507,0.00594410029295454,0.0068375180814217,0,0.140500898507784,0.0162206022578516,0.0145467477751885,0.00414270432459383,0.00455921162488775,0,0,0,0,0.00528042288506863,0.0115124886811745,0.0186302883954726,0.0124419001107118,0.0159994856319394,0.00849595171404108,0.0103162290502624,0.00341015411139406,0.0066169131702738,0.00345424958874048,0.013789245779622,0.0184167103677403,0.00930659712702342,0,0,0.0134357866056322,0.013730225956462,0.0260214868238253,0.00224178327830086,0,0,0.0190378496601629,0.0315392511822797,0.0051461089741816,0.00838309082097742,0.0117599444897799,0.00309295563161119,0.0263543957353782,0.0129982428207788,0.00460600359772608,0,0,0,0,0,0.095460703580563,0,0,0.005475282570495,0.014815195087535,0,0,0,0.00709240957222819,0,0,0.120554574193156,0.074271324595503,0.018734255622458,0.0158670686887134,0.0311708011307803,0.0212367712880673,0.021623291124997,0.0178321630615476,0.00428414807082623,0,0.0196688613697763,0.0114675674336378,0.0319858120675153,0.00661957452107962,0.0162493869788261,0.167956315182436,0,0,0.480682933762284,0.00204776370373108,0.00850389915553517,0.00626238143335183,0.0155025852496231,0.0136340619211839,0.00214187728335593,0.0183923997295892,0.020153770701783,0.0125777681867644,0.0117711558983016,0.0193867487987174,0.0243253706566604,0.011480000421215,0.00691199439583031,0.00418556522081429,0,0.00599207277842711,0.00254016380942609,0.0091200555741297,0.0106719549737799,0.00634983749758357,0,0,0,0.00293288631729645,0.020329210933701,0.0198552798329018,0.0245367113859649,0.0320425689630934,0.0183261523216663,0,0.00751355938625779,0.00452584673019788,0.00340635509803742,0.00695988350993654,0,0,0,0.00259609675069738,0,0.00430053684990213,0.00199841365073706,0,0,0.00141055572843573,0.00957990581703697,0.00359165214970386,0.00658136373256066,0.0315249392948943,0.00177241470658925,0.738912986630544,0.253255216960387,0.0104954989897117,0.0151156882381156,0.0166445803120224,0.0486553604388935,0.0541902563956081,0.0787451242627011,0.321874608069126,0.0868092691055087,0.107972444852538,0.105144497729312,0.136873924932753,0.308134696972506,0.33373082645174,0.462266859007631,0.0116391674049903,0.0151284428986918,0.0136576368518556,0.0242011157017378,0.0276861933368324,0.00995769720166166,0.0180475918006477,0.00912540322296903,0.00881887679492329,0.0108016472689971,0.00939638767467458,0.00279221703825565,0,0,0,0,0.0184790374186727,0.00915111608289733,0.00543805548080564,0.00878006385497333,0.0161240442545995,0.0343496812046805,0.0147432881633845,0.038498599931724,0.0119433618355169,0,0.0254961434858398,0,0.00273194315929295,0,0,0.0184881344904333,0.0136158309738794,0.0188091408703275,0.0254708402631003,0.0241305376118467,0.0213564589679692,0.0276183413562683,0.0215697211912192,0.0227179238574385,0.016638018285244,0.0157183971705182,0,0,0.0121534260259464,0.00896299814932682,0,0.0122209567075048,0.0220957985197118,0.0164077460414113,0.0129660945996033,0.0160167294772526,0.0135459842085214,0.0159577476288533,0.0261753032662935,0.004639521230829,0.014150958549267,0.0140229804835773,0.0445799794438214,0.00593078966247423,0.0105643529924115,0.02039632061705,0.01528669241902,0.0274637499892152,0.0222436175715979,0.0168228959679113,0.00839841715720154,0.00485083983250621,0.0583724781235284,0,0.01103491323045,0,0.0130266576313777,0,0.00939735441778808,0.00299602050618165,0.0124910280698433,0.00351413501652256,0.0106736091317014,0.00297005173074119,0.00826972180945102,0.0167417083586575,0,0.00347676840910867,0.0164007662877396,0.058005089173441,0.027272128625909,0.0382606765299916,0.0273626846912972,0.0254638092610787,0.286852524126554,0.00923427408633047,0.0338841332983685,0.00625302552444433,0.00307456822749447,0.0348868909080617,0.0626115625935857,0.0524002134501316,0.00284074396089791,0.00474052968469908,0,0.336940104570877,0.0123412113475016,0.0222159485756127,0.0481922601392112,0.0537657744288754,0.0798024832700175,0.0216585098201145,0.0720318795321096,0.267979041331683,0.12731637423648,0.0146152935014036,0,0.00922702536735198,0.00919115125498425,0.0122901363796828,0.0112138434269023,0.0182987796896736,0.00545832199397762,0.0162493628392597,0.00633817655064633,0,0,0.0945134746418256,0,0.0293359876499661,0.033943006863228,0.0380174897205899,0.0421467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spanning protein tyrosine kinase activity;8.11094323245837e-05;17179,15162,12169!GO:0007242;intracellular signaling cascade;0.00196897682908386;17179,15162,12169,326623,71130!GO:0004713;protein-tyrosine kinase activity;0.00196897682908386;17179,15162,12169!GO:0007165;signal transduction;0.00713790286926552;246709,17179,15162,233080,12169,326623,71130!GO:0007154;cell communication;0.00854678678617675;246709,17179,15162,233080,12169,326623,71130!GO:0016299;regulator of G-protein signaling activity;0.0192255013928163;246709!GO:0004672;protein kinase activity;0.032023213734179;17179,15162,12169!GO:0007250;activation of NF-kappaB-inducing kinase;0.032023213734179;326623!GO:0006468;protein amino acid phosphorylation;0.032023213734179;17179,15162,12169!GO:0016773;phosphotransferase activity, alcohol group as acceptor;0.033607780848479;17179,15162,12169!GO:0016310;phosphorylation;0.033607780848479;17179,15162,12169!GO:0045744;negative regulation of G-protein coupled receptor protein signaling pathway;0.033607780848479;246709!GO:0006793;phosphorus metabolic process;0.0452943172759087;17179,15162,12169!GO:0006796;phosphate metabolic 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|gostat_on_MCL_coexpression=GO:0004715;non-membrane spanning protein tyrosine kinase activity;8.11094323245837e-05;17179,15162,12169!GO:0007242;intracellular signaling cascade;0.00196897682908386;17179,15162,12169,326623,71130!GO:0004713;protein-tyrosine kinase activity;0.00196897682908386;17179,15162,12169!GO:0007165;signal transduction;0.00713790286926552;246709,17179,15162,233080,12169,326623,71130!GO:0007154;cell communication;0.00854678678617675;246709,17179,15162,233080,12169,326623,71130!GO:0016299;regulator of G-protein signaling activity;0.0192255013928163;246709!GO:0004672;protein kinase activity;0.032023213734179;17179,15162,12169!GO:0007250;activation of NF-kappaB-inducing kinase;0.032023213734179;326623!GO:0006468;protein amino acid phosphorylation;0.032023213734179;17179,15162,12169!GO:0016773;phosphotransferase activity, alcohol group as acceptor;0.033607780848479;17179,15162,12169!GO:0016310;phosphorylation;0.033607780848479;17179,15162,12169!GO:0045744;negative regulation of G-protein coupled receptor protein signaling pathway;0.033607780848479;246709!GO:0006793;phosphorus metabolic process;0.0452943172759087;17179,15162,12169!GO:0006796;phosphate metabolic process;0.0452943172759087;17179,15162,12169!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005409!1.16e-20!47;UBERON:0000160!1.66e-20!31;UBERON:0000344!5.55e-17!15;UBERON:0001242!5.82e-12!13;UBERON:0000060!5.82e-12!13;UBERON:0001262!5.82e-12!13;UBERON:0004786!5.82e-12!13;UBERON:0001007!4.11e-11!116;UBERON:0001555!4.11e-11!116;UBERON:0007026!4.11e-11!116;UBERON:0004119!7.64e-11!118;UBERON:0000925!7.64e-11!118;UBERON:0006595!7.64e-11!118;UBERON:0004923!5.34e-10!24;UBERON:0003350!2.33e-09!9;UBERON:0004808!2.33e-09!9;UBERON:0001277!2.33e-09!9;UBERON:0004921!5.97e-09!114;UBERON:0001962!6.90e-08!2;UBERON:0001961!6.90e-08!2;UBERON:0001744!6.90e-08!2;UBERON:0000485!1.37e-07!11
|tfbs_overrepresentation_for_novel_motifs=0.10298,0.242043,0.300372,1.29157,0.161423,0.419638,0.192737,0.612769,0.967029,0.401022,0.163789,0.184641,0.369722,0.20111,0.404084,0,0.346366,0.352159,0.165057,0.60644,0.91454,0.397987,0.200489,0.653803,0.310745,0.220337,0.307294,0.884926,0.0588695,0.578277,0.138971,0.430274,0.0382637,0.258731,0.0478417,0.257253,0.0352642,0.182233,0.840626,0.0212909,0.157073,0.437962,0.120149,0.720278,0.0388978,0.119992,0.283619,0.157367,0.26283,0.473837,0.332337,0.239655,0.190262,0.553844,0.569458,0.206047,1.28613,0.176187,0.48745,0.204634,0.413329,0.246553,1.4193,0.323367,0.213815,0.355898,0.693798,1.02539,1.05417,0.883956,0.27498,0.94768,0.00863608,0.599674,0.0467969,0.241392,1.71756,0.274952,0.398928,0.0738984,0.954206,0.360462,0.245495,0.35158,1.24289,0.000774753,0.916247,0.0953467,0.287376,1.18318,0.758722,0.501285,1.12313,0.3811,0.0276224,0.0994305,0.362313,0.44358,0.283814,0.708123,0.140916,0.430036,0.538321,0.885435,0.33197,0.141825,0.38053,0.154838,0.263369,0.0727888,0.0992584,1.33434,0.258506,0.167109,0.765328,0.356538,0.05807,0.403561,0.347417,0.321151,0.604565,0.827242,0.631228,0.274265,0.816304,0.40202,0.198291,0.4354,0.692394,0.387426,0.523273,0.122184,0.665113,0.215582,0.785621,1.04532,0.107493,0.44012,0.739526,1.5459,1.15207,0.698162,0.651432,0.439187,0.326804,0.438656,0.286009,1.50665,0.714598,0.664553,0.210657,0.000743183,0.555246,0.480297,1.15665,0.629009,0.675146,0.0522118,0.681778,0.107341,0.748413,0.496177,0.402392,0.664909,0.86614,0.603124,0.931461,0.540411,0.022023
|tfbs_overrepresentation_jaspar=MA0003.1;0.000310914,MA0004.1;0.126659,MA0006.1;0.0460466,MA0007.1;0.376537,MA0009.1;0.452863,MA0014.1;0.000122002,MA0017.1;0.205754,MA0019.1;0.818593,MA0024.1;0.415603,MA0025.1;0.660968,MA0027.1;2.04174,MA0028.1;0.0499059,MA0029.1;0.397373,MA0030.1;0.402861,MA0031.1;0.373333,MA0038.1;0.62805,MA0040.1;0.463641,MA0041.1;0.290933,MA0042.1;0.273359,MA0043.1;0.53743,MA0046.1;0.483941,MA0048.1;0.023533,MA0050.1;0.149886,MA0051.1;0.226644,MA0052.1;0.47061,MA0055.1;0.232159,MA0056.1;0,MA0057.1;0.14014,MA0058.1;0.0765185,MA0059.1;0.0823381,MA0060.1;0.0949887,MA0061.1;0.537954,MA0063.1;0,MA0066.1;0.212546,MA0067.1;0.764133,MA0068.1;0.0650147,MA0069.1;0.470904,MA0070.1;0.462521,MA0071.1;0.456242,MA0072.1;0.455219,MA0073.1;0.0007102,MA0074.1;0.550954,MA0076.1;0.064121,MA0077.1;2.90324,MA0078.1;0.250627,MA0081.1;0.644573,MA0083.1;0.536725,MA0084.1;1.07765,MA0087.1;0.4987,MA0088.1;0.149641,MA0089.1;0,MA0090.1;0.708683,MA0091.1;1.34177,MA0092.1;0.107655,MA0093.1;0.0530878,MA0095.1;0,MA0098.1;0,MA0100.1;0.180237,MA0101.1;0.292678,MA0103.1;0.476679,MA0105.1;0.118663,MA0106.1;0.256379,MA0107.1;0.462865,MA0108.2;0.85894,MA0109.1;0,MA0111.1;0.369101,MA0113.1;0.2357,MA0114.1;0.530742,MA0115.1;0.539917,MA0116.1;0.174756,MA0117.1;0.511373,MA0119.1;0.293473,MA0122.1;0.528896,MA0124.1;1.7,MA0125.1;0.646095,MA0130.1;0,MA0131.1;0.299487,MA0132.1;0,MA0133.1;0,MA0135.1;0.569948,MA0136.1;0.201456,MA0139.1;0.0699025,MA0140.1;0.532112,MA0141.1;0.24332,MA0142.1;1.69142,MA0143.1;1.28115,MA0144.1;0.540257,MA0145.1;0.171363,MA0146.1;0.0147284,MA0147.1;0.0335355,MA0148.1;0.836385,MA0149.1;0.0894222,MA0062.2;0.0449909,MA0035.2;1.63216,MA0039.2;0.0131673,MA0138.2;0.796689,MA0002.2;1.67165,MA0137.2;0.0677978,MA0104.2;0.0185242,MA0047.2;1.17521,MA0112.2;0.00977802,MA0065.2;0.461871,MA0150.1;0.376372,MA0151.1;0,MA0152.1;1.1755,MA0153.1;0.584906,MA0154.1;0.0704998,MA0155.1;0.354426,MA0156.1;0.227959,MA0157.1;0.335532,MA0158.1;0,MA0159.1;0.036714,MA0160.1;0.427566,MA0161.1;0,MA0162.1;0.0223877,MA0163.1;0.00646064,MA0164.1;0.583987,MA0080.2;0.806441,MA0018.2;0.208409,MA0099.2;0.288477,MA0079.2;1.27548e-07,MA0102.2;1.12863,MA0258.1;0.107482,MA0259.1;0.296386,MA0442.1;0
}}

Latest revision as of 15:07, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80720893..80720912,+p4@Matk
Mm9::chr11:3431562..3431575,-p@chr11:3431562..3431575
-
Mm9::chr11:95885854..95885872,+p1@Gip
Mm9::chr17:35218137..35218148,-p@chr17:35218137..35218148
-
Mm9::chr17:37030973..37030980,-p@chr17:37030973..37030980
-
Mm9::chr19:40905054..40905084,+p@chr19:40905054..40905084
+
Mm9::chr1:146024315..146024326,-p2@Rgs13
Mm9::chr1:146024389..146024411,-p1@Rgs13
Mm9::chr1:153099939..153099982,-p@chr1:153099939..153099982
-
Mm9::chr2:152933392..152933409,+p@chr2:152933392..152933409
+
Mm9::chr2:152933438..152933445,+p@chr2:152933438..152933445
+
Mm9::chr3:144759807..144759821,+p@chr3:144759807..144759821
+
Mm9::chr4:63406089..63406095,-p1@Tnfsf15
Mm9::chr6:145093993..145094003,+p6@Lrmp
Mm9::chr6:72471665..72471668,-p6@Sh2d6
Mm9::chr6:72471687..72471701,-p1@Sh2d6
Mm9::chr6:72471704..72471733,-p2@Sh2d6
Mm9::chr7:150279910..150279946,-p@chr7:150279910..150279946
-
Mm9::chr7:31641206..31641219,-p1@Ffar3
Mm9::chr7:53358071..53358073,+p@chr7:53358071..53358073
+
Mm9::chr8:120027901..120027907,+p@chr8:120027901..120027907
+
Mm9::chr9:51137003..51137028,-p1@1810046K07Rik
Mm9::chr9:54381927..54381934,+p1@Sh2d7
Mm9::chrX:160688308..160688314,-p3@Bmx


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:0004715non-membrane spanning protein tyrosine kinase activity8.11094323245837e-05
GO:0007242intracellular signaling cascade0.00196897682908386
GO:0004713protein-tyrosine kinase activity0.00196897682908386
GO:0007165signal transduction0.00713790286926552
GO:0007154cell communication0.00854678678617675
GO:0016299regulator of G-protein signaling activity0.0192255013928163
GO:0004672protein kinase activity0.032023213734179
GO:0007250activation of NF-kappaB-inducing kinase0.032023213734179
GO:0006468protein amino acid phosphorylation0.032023213734179
GO:0016773phosphotransferase activity, alcohol group as acceptor0.033607780848479
GO:0016310phosphorylation0.033607780848479
GO:0045744negative regulation of G-protein coupled receptor protein signaling pathway0.033607780848479
GO:0006793phosphorus metabolic process0.0452943172759087
GO:0006796phosphate metabolic process0.0452943172759087



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>


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)
MA0003.10.000310914
MA0004.10.126659
MA0006.10.0460466
MA0007.10.376537
MA0009.10.452863
MA0014.10.000122002
MA0017.10.205754
MA0019.10.818593
MA0024.10.415603
MA0025.10.660968
MA0027.12.04174
MA0028.10.0499059
MA0029.10.397373
MA0030.10.402861
MA0031.10.373333
MA0038.10.62805
MA0040.10.463641
MA0041.10.290933
MA0042.10.273359
MA0043.10.53743
MA0046.10.483941
MA0048.10.023533
MA0050.10.149886
MA0051.10.226644
MA0052.10.47061
MA0055.10.232159
MA0056.10
MA0057.10.14014
MA0058.10.0765185
MA0059.10.0823381
MA0060.10.0949887
MA0061.10.537954
MA0063.10
MA0066.10.212546
MA0067.10.764133
MA0068.10.0650147
MA0069.10.470904
MA0070.10.462521
MA0071.10.456242
MA0072.10.455219
MA0073.10.0007102
MA0074.10.550954
MA0076.10.064121
MA0077.12.90324
MA0078.10.250627
MA0081.10.644573
MA0083.10.536725
MA0084.11.07765
MA0087.10.4987
MA0088.10.149641
MA0089.10
MA0090.10.708683
MA0091.11.34177
MA0092.10.107655
MA0093.10.0530878
MA0095.10
MA0098.10
MA0100.10.180237
MA0101.10.292678
MA0103.10.476679
MA0105.10.118663
MA0106.10.256379
MA0107.10.462865
MA0108.20.85894
MA0109.10
MA0111.10.369101
MA0113.10.2357
MA0114.10.530742
MA0115.10.539917
MA0116.10.174756
MA0117.10.511373
MA0119.10.293473
MA0122.10.528896
MA0124.11.7
MA0125.10.646095
MA0130.10
MA0131.10.299487
MA0132.10
MA0133.10
MA0135.10.569948
MA0136.10.201456
MA0139.10.0699025
MA0140.10.532112
MA0141.10.24332
MA0142.11.69142
MA0143.11.28115
MA0144.10.540257
MA0145.10.171363
MA0146.10.0147284
MA0147.10.0335355
MA0148.10.836385
MA0149.10.0894222
MA0062.20.0449909
MA0035.21.63216
MA0039.20.0131673
MA0138.20.796689
MA0002.21.67165
MA0137.20.0677978
MA0104.20.0185242
MA0047.21.17521
MA0112.20.00977802
MA0065.20.461871
MA0150.10.376372
MA0151.10
MA0152.11.1755
MA0153.10.584906
MA0154.10.0704998
MA0155.10.354426
MA0156.10.227959
MA0157.10.335532
MA0158.10
MA0159.10.036714
MA0160.10.427566
MA0161.10
MA0162.10.0223877
MA0163.10.00646064
MA0164.10.583987
MA0080.20.806441
MA0018.20.208409
MA0099.20.288477
MA0079.21.27548e-07
MA0102.21.12863
MA0258.10.107482
MA0259.10.296386
MA0442.10
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