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MCL coexpression mm9:710: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0002320!1.07e-11!46;CL:0000134!1.07e-11!46;CL:0000988!1.37e-10!32;CL:0002032!1.37e-10!32;CL:0000037!1.37e-10!32;CL:0000566!1.37e-10!32;CL:0000837!1.37e-10!32;CL:0000219!3.41e-10!54;CL:0002031!1.28e-08!25;CL:0000738!1.90e-08!17;CL:0002087!1.90e-08!17;CL:0000838!4.02e-08!12;CL:0000084!1.94e-07!11;CL:0000827!1.94e-07!11;CL:0000791!5.67e-07!9;CL:0000789!5.67e-07!9;CL:0002420!5.67e-07!9;CL:0002419!5.67e-07!9;CL:0000790!5.67e-07!9;CL:0000542!9.17e-07!13;CL:0000051!9.17e-07!13
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.62e-19!48;UBERON:0002405!1.62e-19!48;UBERON:0002390!7.69e-18!45;UBERON:0003061!7.69e-18!45;UBERON:0001007!7.37e-15!116;UBERON:0001555!7.37e-15!116;UBERON:0007026!7.37e-15!116;UBERON:0004119!7.55e-15!118;UBERON:0000925!7.55e-15!118;UBERON:0006595!7.55e-15!118;UBERON:0004921!5.62e-14!114;UBERON:0002384!1.07e-11!46;UBERON:0000490!1.35e-11!66;UBERON:0000077!1.33e-10!35;UBERON:0004177!2.74e-10!29;UBERON:0005057!2.74e-10!29;UBERON:0003929!5.53e-10!55;UBERON:0005911!6.22e-10!69;UBERON:0003081!7.49e-10!87;UBERON:0000072!1.93e-09!27;UBERON:0002204!2.10e-09!32;UBERON:0002370!2.86e-09!23;UBERON:0000974!2.86e-09!23;UBERON:0004807!2.86e-09!23;UBERON:0005058!2.86e-09!23;UBERON:0003351!2.86e-09!23;UBERON:0009113!2.86e-09!23;UBERON:0003295!2.86e-09!23;UBERON:0009722!2.86e-09!23;UBERON:0005562!2.86e-09!23;UBERON:0007690!2.86e-09!23;UBERON:0003408!5.38e-09!24;UBERON:0006562!7.94e-09!24;UBERON:0001557!7.94e-09!24;UBERON:0001042!7.94e-09!24;UBERON:0008814!7.94e-09!24;UBERON:0009145!7.94e-09!24;UBERON:0002371!1.68e-08!16;UBERON:0000065!1.72e-08!41;UBERON:0001004!2.31e-08!42;UBERON:0001041!3.81e-08!80;UBERON:0001474!1.85e-07!22;UBERON:0004765!1.85e-07!22;UBERON:0001434!1.85e-07!22;UBERON:0000063!3.23e-07!35;UBERON:0004923!4.54e-07!24;UBERON:0000926!6.60e-07!120;UBERON:0004120!6.60e-07!120;UBERON:0006603!6.60e-07!120
|tfbs_overrepresentation_for_novel_motifs=0.860199,0.178895,0.807108,0.360062,0.200163,0.975411,0.458558,0.392928,0.411053,0.10445,0.417132,0.447169,0.124608,1.18563,0.214197,0,0.656089,0.19356,0.364803,0.451901,0.732601,0.336916,0.469335,0.198877,0.304728,0.496413,0.349241,1.01819,0.238759,0.967915,0.379806,0.754912,0.191698,0.31333,1.80612,0.102262,0.184038,1.12869,0.166348,0.442131,0.196807,0.999982,0.56316,0.617704,0.434259,0.923221,0.578773,1.05036,0.479635,0.677281,1.54311,0.522137,0.259389,2.07004,0.911367,0.47699,0.249055,0.435119,0.332535,0.47505,0.735292,0.531188,0.433822,0.628155,0.487593,1.60248,1.04613,1.3932,0.730718,1.24673,0.281085,0.80439,0.155003,0.944464,0.659328,0.300089,0.313198,0.567793,0.718494,0.268962,1.31277,0.673009,0.529804,0.380754,0.830765,0.538155,0.0697823,0.572901,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.490417,0.149272,0.777003,0.770215,0.57902,0.50528,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.750985,0.736223,1.52799,2.03846,0.26996,0.421988,1.12221,1.07996,0.409202,1.69868,1.58124,1.02287,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,1.22806,1.14365,0.0358067,1.57798,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,1.00091,0.581788,1.88287,0.331322,0.201635,0.275954,0.129005,0.895708,0.46758,0.489108,0.976367,0.523103,0.224422,0.319291,1.57707,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.18312,0.445669,0.19482
|tfbs_overrepresentation_jaspar=MA0003.1;0.347165,MA0004.1;0.360508,MA0006.1;0.604851,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;1.43076,MA0017.1;0.233089,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;2.57895,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.79301,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;0.236433,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.0660514,MA0056.1;0,MA0057.1;0.216209,MA0058.1;0.273976,MA0059.1;0.28489,MA0060.1;1.40918,MA0061.1;2.21331,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.836551,MA0069.1;1.87961,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;0.0215953,MA0074.1;0.451832,MA0076.1;1.28862,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;0.623059,MA0089.1;0,MA0090.1;0.877277,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.226349,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;2.21397,MA0103.1;0.242398,MA0105.1;1.56265,MA0106.1;0.543967,MA0107.1;1.92665,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.342068,MA0113.1;0.516916,MA0114.1;0.167085,MA0115.1;0.878749,MA0116.1;0.604438,MA0117.1;0.846964,MA0119.1;1.44977,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;0.598671,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;0.121562,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.976447,MA0145.1;0.664015,MA0146.1;0.0389394,MA0147.1;0.179496,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;2.83024,MA0035.2;0.44524,MA0039.2;4.87692,MA0138.2;0.590987,MA0002.2;0.391079,MA0137.2;0.713675,MA0104.2;0.828906,MA0047.2;0.495607,MA0112.2;0.163154,MA0065.2;0.163769,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.232525,MA0155.1;0.416651,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;1.6576,MA0160.1;0.378276,MA0161.1;0,MA0162.1;0.730425,MA0163.1;0.043065,MA0164.1;0.471016,MA0080.2;0.669221,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;2.09889,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;0.50935,MA0442.1;0
}}

Latest revision as of 15:45, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:49016816..49016846,+p2@Zfp62
Mm9::chr11:6421013..6421027,+p@chr11:6421013..6421027
+
Mm9::chr17:35516553..35516582,+p1@H2-Q4
Mm9::chr17:45692642..45692663,+p1@Nfkbie
Mm9::chr17:45692676..45692695,+p2@Nfkbie
Mm9::chr4:124805092..124805135,-p2@Zc3h12a
Mm9::chr4:129488217..129488231,-p@chr4:129488217..129488231
-
Mm9::chr6:117856954..117857026,+p5@Hnrnpf
Mm9::chr6:122258987..122259036,+p1@M6pr
Mm9::chr7:132695774..132695820,+p1@Il4ra


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:0005159insulin-like growth factor receptor binding0.0221857021476894
GO:0018445prothoracicotrophic hormone activity0.0221857021476894



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
hemolymphoid system1.62e-1948
immune system1.62e-1948
hematopoietic system7.69e-1845
blood island7.69e-1845
digestive system7.37e-15116
digestive tract7.37e-15116
primitive gut7.37e-15116
endoderm-derived structure7.55e-15118
endoderm7.55e-15118
presumptive endoderm7.55e-15118
subdivision of digestive tract5.62e-14114
connective tissue1.07e-1146
unilaminar epithelium1.35e-1166
mixed endoderm/mesoderm-derived structure1.33e-1035
hemopoietic organ2.74e-1029
immune organ2.74e-1029
gut epithelium5.53e-1055
endo-epithelium6.22e-1069
lateral plate mesoderm7.49e-1087
segment of respiratory tract1.93e-0927
musculoskeletal system2.10e-0932
thymus2.86e-0923
neck2.86e-0923
respiratory system epithelium2.86e-0923
hemolymphoid system gland2.86e-0923
pharyngeal epithelium2.86e-0923
thymic region2.86e-0923
pharyngeal gland2.86e-0923
entire pharyngeal arch endoderm2.86e-0923
thymus primordium2.86e-0923
early pharyngeal endoderm2.86e-0923
gland of gut5.38e-0924
pharynx7.94e-0924
upper respiratory tract7.94e-0924
chordate pharynx7.94e-0924
pharyngeal arch system7.94e-0924
pharyngeal region of foregut7.94e-0924
bone marrow1.68e-0816
respiratory tract1.72e-0841
respiratory system2.31e-0842
foregut3.81e-0880
bone element1.85e-0722
skeletal element1.85e-0722
skeletal system1.85e-0722
organ segment3.23e-0735
organ component layer4.54e-0724
mesoderm6.60e-07120
mesoderm-derived structure6.60e-07120
presumptive mesoderm6.60e-07120


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)
MA0003.10.347165
MA0004.10.360508
MA0006.10.604851
MA0007.10.346734
MA0009.10.780842
MA0014.11.43076
MA0017.10.233089
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.12.57895
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.79301
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.10.236433
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.0660514
MA0056.10
MA0057.10.216209
MA0058.10.273976
MA0059.10.28489
MA0060.11.40918
MA0061.12.21331
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.836551
MA0069.11.87961
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.10.0215953
MA0074.10.451832
MA0076.11.28862
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.623059
MA0089.10
MA0090.10.877277
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.12.21397
MA0103.10.242398
MA0105.11.56265
MA0106.10.543967
MA0107.11.92665
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.167085
MA0115.10.878749
MA0116.10.604438
MA0117.10.846964
MA0119.11.44977
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.10.598671
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.10.121562
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.976447
MA0145.10.664015
MA0146.10.0389394
MA0147.10.179496
MA0148.10.375491
MA0149.10.2978
MA0062.22.83024
MA0035.20.44524
MA0039.24.87692
MA0138.20.590987
MA0002.20.391079
MA0137.20.713675
MA0104.20.828906
MA0047.20.495607
MA0112.20.163154
MA0065.20.163769
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.232525
MA0155.10.416651
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.11.6576
MA0160.10.378276
MA0161.10
MA0162.10.730425
MA0163.10.043065
MA0164.10.471016
MA0080.20.669221
MA0018.20.480226
MA0099.20.584892
MA0079.22.09889
MA0102.21.49914
MA0258.10.156336
MA0259.10.50935
MA0442.10
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