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MCL coexpression mm9:298: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000153!5.67e-08!43;UBERON:0007811!1.40e-07!36;UBERON:0000065!1.97e-07!41;UBERON:0001004!2.68e-07!42;UBERON:0004177!2.73e-07!29;UBERON:0005057!2.73e-07!29;UBERON:0000077!6.56e-07!35
|ontology_enrichment_uberon=UBERON:0000153!5.67e-08!43;UBERON:0007811!1.40e-07!36;UBERON:0000065!1.97e-07!41;UBERON:0001004!2.68e-07!42;UBERON:0004177!2.73e-07!29;UBERON:0005057!2.73e-07!29;UBERON:0000077!6.56e-07!35
|tfbs_overrepresentation_for_novel_motifs=0.591785,0.0214946,0.531928,0.338886,0.125245,0.359101,0.493739,0.051338,0.525465,0.995728,0.843247,0.156977,0.140984,0.512825,0.141341,0,0.833764,0.28293,0.00830799,0.461593,0.450817,0.284714,4.64324,0.030106,0.258457,1.05959,0.00731067,0.389073,1.06282,0.448036,0.368848,0.390688,0.278799,0.192,0.599215,0.157309,1.56259,2.81522,0.698183,0.879506,0.290168,0.376228,0.011766,0.333507,0.19906,0.32356,0.697098,0.81779,0.020961,0.696619,0.296304,1.1309,0.0586377,0.511069,0.526356,1.5954,0.183928,0.455754,0.0998872,1.00074,0.97729,0.61508,0.0648948,1.42919,3.09031,0.318903,0.648538,0.976882,0.370478,0.836509,1.27749,0.512402,3.30516,0.555978,0.358128,0.177468,0.345431,0.241622,0.360359,0.798977,0.0113722,0.32329,0.213792,0.467951,0.455476,0.750187,0.0493039,1.23562,1.30281,1.13385,0.712592,0.459726,0.401262,0.032222,2.81817,0.369361,1.805,0.403591,0.25003,0.111549,0.0253676,0.390457,0.495886,0.29676,0.295953,1.80149,1.62543,0.406177,0.470494,2.22936,0.273137,0.497436,0.802694,1.38182,0.719117,0.529908,0.452141,1.15674,0.31076,0.255342,0.560777,0.747996,0.559259,0.240971,0.769516,0.363346,0.169628,1.8097,0.647155,0.314565,0.481183,3.61813,0.620289,0.185736,0.739171,1.0549,0.293295,0.118762,0.693638,1.49553,1.10287,0.652839,0.199449,0.399329,0.791415,1.80571,0.252115,1.45635,0.296414,1.26217,0.0671312,1.49905,0.512441,0.636231,0.185128,0.584782,1.13359,0.353262,0.279074,0.610752,0.702412,0.454746,0.363706,0.270234,0.288496,0.180287,0.106601,0.155999,0.839108
|tfbs_overrepresentation_for_novel_motifs=0.591785,0.0214946,0.531928,0.338886,0.125245,0.359101,0.493739,0.051338,0.525465,0.995728,0.843247,0.156977,0.140984,0.512825,0.141341,0,0.833764,0.28293,0.00830799,0.461593,0.450817,0.284714,4.64324,0.030106,0.258457,1.05959,0.00731067,0.389073,1.06282,0.448036,0.368848,0.390688,0.278799,0.192,0.599215,0.157309,1.56259,2.81522,0.698183,0.879506,0.290168,0.376228,0.011766,0.333507,0.19906,0.32356,0.697098,0.81779,0.020961,0.696619,0.296304,1.1309,0.0586377,0.511069,0.526356,1.5954,0.183928,0.455754,0.0998872,1.00074,0.97729,0.61508,0.0648948,1.42919,3.09031,0.318903,0.648538,0.976882,0.370478,0.836509,1.27749,0.512402,3.30516,0.555978,0.358128,0.177468,0.345431,0.241622,0.360359,0.798977,0.0113722,0.32329,0.213792,0.467951,0.455476,0.750187,0.0493039,1.23562,1.30281,1.13385,0.712592,0.459726,0.401262,0.032222,2.81817,0.369361,1.805,0.403591,0.25003,0.111549,0.0253676,0.390457,0.495886,0.29676,0.295953,1.80149,1.62543,0.406177,0.470494,2.22936,0.273137,0.497436,0.802694,1.38182,0.719117,0.529908,0.452141,1.15674,0.31076,0.255342,0.560777,0.747996,0.559259,0.240971,0.769516,0.363346,0.169628,1.8097,0.647155,0.314565,0.481183,3.61813,0.620289,0.185736,0.739171,1.0549,0.293295,0.118762,0.693638,1.49553,1.10287,0.652839,0.199449,0.399329,0.791415,1.80571,0.252115,1.45635,0.296414,1.26217,0.0671312,1.49905,0.512441,0.636231,0.185128,0.584782,1.13359,0.353262,0.279074,0.610752,0.702412,0.454746,0.363706,0.270234,0.288496,0.180287,0.106601,0.155999,0.839108
|tfbs_overrepresentation_jaspar=MA0003.1;1.35674,MA0004.1;0.104042,MA0006.1;0.321056,MA0007.1;0.656832,MA0009.1;0.412602,MA0014.1;4.27715,MA0017.1;0.0425137,MA0019.1;0.268299,MA0024.1;0.982128,MA0025.1;0.616209,MA0027.1;1.99083,MA0028.1;0.964323,MA0029.1;0.358857,MA0030.1;0.364159,MA0031.1;0.335674,MA0038.1;0.190128,MA0040.1;0.423075,MA0041.1;0.0680579,MA0042.1;0.224462,MA0043.1;0.495015,MA0046.1;0.442826,MA0048.1;0.366277,MA0050.1;0.12507,MA0051.1;0.196084,MA0052.1;0.429851,MA0055.1;0.0200406,MA0056.1;0,MA0057.1;1.93668,MA0058.1;0.0597941,MA0059.1;0.231081,MA0060.1;0.889814,MA0061.1;0.229521,MA0063.1;0,MA0066.1;0.53876,MA0067.1;0.717937,MA0068.1;0.10147,MA0069.1;0.430137,MA0070.1;0.421986,MA0071.1;0.124599,MA0072.1;0.414891,MA0073.1;0.00426612,MA0074.1;0.160032,MA0076.1;1.11784,MA0077.1;0.396883,MA0078.1;0.218627,MA0081.1;0.936282,MA0083.1;0.494326,MA0084.1;1.02883,MA0087.1;0.457205,MA0088.1;2.04408,MA0089.1;0,MA0090.1;0.0869074,MA0091.1;0.110977,MA0092.1;0.29369,MA0093.1;0.0399156,MA0095.1;0,MA0098.1;0,MA0100.1;0.907524,MA0101.1;0.519199,MA0103.1;0.0462215,MA0105.1;0.52902,MA0106.1;0.224053,MA0107.1;0.168906,MA0108.2;0.285422,MA0109.1;0,MA0111.1;0.0938213,MA0113.1;0.20458,MA0114.1;0.0900443,MA0115.1;0.497446,MA0116.1;0.583641,MA0117.1;0.469566,MA0119.1;0.242709,MA0122.1;0.486676,MA0124.1;0.668899,MA0125.1;0.601578,MA0130.1;0,MA0131.1;2.07199,MA0132.1;0,MA0133.1;0,MA0135.1;0.526836,MA0136.1;0.513613,MA0139.1;0.0490456,MA0140.1;0.464908,MA0141.1;0.197414,MA0142.1;0.324241,MA0143.1;0.215799,MA0144.1;0.230788,MA0145.1;0.114967,MA0146.1;1.74485,MA0147.1;0.473869,MA0148.1;0.112635,MA0149.1;1.8872,MA0062.2;1.82797,MA0035.2;0.155719,MA0039.2;4.45988,MA0138.2;0.259078,MA0002.2;0.139327,MA0137.2;0.430805,MA0104.2;0.319656,MA0047.2;0.18962,MA0112.2;0.500556,MA0065.2;0.0546357,MA0150.1;0.0963127,MA0151.1;0,MA0152.1;0.189691,MA0153.1;0.541494,MA0154.1;0.212555,MA0155.1;0.405027,MA0156.1;0.724462,MA0157.1;0.299365,MA0158.1;0,MA0159.1;0.805512,MA0160.1;0.114259,MA0161.1;0,MA0162.1;2.02296,MA0163.1;0.554882,MA0164.1;0.514179,MA0080.2;0.169853,MA0018.2;3.04418,MA0099.2;0.254459,MA0079.2;5.52854,MA0102.2;1.07954,MA0258.1;0.203197,MA0259.1;0.720568,MA0442.1;0
}}
}}

Revision as of 11:31, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:20032330..20032345,+p3@Bclaf1
Mm9::chr10:40602879..40602936,-p1@Cdc40
Mm9::chr10:7512695..7512734,+p1@Ppil4
Mm9::chr11:104303623..104303641,-p4@1700081L11Rik
Mm9::chr11:23795208..23795280,-p1@Papolg
Mm9::chr11:51076623..51076699,+p1@Clk4
Mm9::chr12:82046510..82046528,+p1@Gm12966
p1@Srsf5
Mm9::chr13:112280043..112280098,-p1@Gpbp1
Mm9::chr18:67884180..67884213,-p2@Ptpn2
Mm9::chr1:55084221..55084250,-p1@Sf3b1
Mm9::chr1:58480851..58480872,-p1@Clk1
Mm9::chr1:58480886..58480908,-p2@Clk1
Mm9::chr2:10002227..10002245,+p1@Kin
Mm9::chr2:156005871..156005937,-p1@Rbm39
Mm9::chr2:34657856..34657911,+p1@uc008jiw.1
Mm9::chr3:30501539..30501575,+p@chr3:30501539..30501575
+
Mm9::chr5:148241729..148241793,+p1@Pan3
Mm9::chr5:20457587..20457642,-p1@Rsbn1l
Mm9::chr5:22939123..22939162,-p1@uc008wpw.1
p1@uc008wpx.1
Mm9::chr5:53981912..53981942,+p1@Rbpj
Mm9::chr5:87233306..87233322,+p2@Ythdc1
Mm9::chr5:9161692..9161762,-p1@Dmtf1
Mm9::chr6:120314411..120314466,+p2@Kdm5a
Mm9::chr7:80686605..80686623,-p2@Chd2
Mm9::chr7:80686624..80686644,-p1@Chd2
Mm9::chr8:72240749..72240811,-p1@Zfp869
Mm9::chrX:39503903..39503928,+p3@Stag2


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:0005634nucleus3.76419046431649e-05
GO:0043283biopolymer metabolic process0.000311836934344768
GO:0043170macromolecule metabolic process0.000497536975592701
GO:0043231intracellular membrane-bound organelle0.000586687245999991
GO:0043227membrane-bound organelle0.000586687245999991
GO:0003676nucleic acid binding0.000746427899461023
GO:0016070RNA metabolic process0.000774831726398036
GO:0016485protein processing0.00127511598646046
GO:0006397mRNA processing0.0019505498710537
GO:0044238primary metabolic process0.0019505498710537
GO:0044237cellular metabolic process0.0019505498710537
GO:0010467gene expression0.0019505498710537
GO:0043229intracellular organelle0.0019505498710537
GO:0043226organelle0.0019505498710537
GO:0016071mRNA metabolic process0.0019505498710537
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00383249314735907
GO:0003677DNA binding0.00418382364513257
GO:0044424intracellular part0.00494269684193766
GO:0006396RNA processing0.00494269684193766
GO:0006350transcription0.00494269684193766
GO:0046777protein amino acid autophosphorylation0.00615239353534538
GO:0016540protein autoprocessing0.00660974729994499
GO:0005622intracellular0.00668764818428192
GO:0018212peptidyl-tyrosine modification0.0143628569552499
GO:0018108peptidyl-tyrosine phosphorylation0.0143628569552499
GO:0006355regulation of transcription, DNA-dependent0.0143628569552499
GO:0006351transcription, DNA-dependent0.0145152041548976
GO:0032774RNA biosynthetic process0.0145152041548976
GO:0045449regulation of transcription0.0160271656701653
GO:0003723RNA binding0.0160271656701653
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0172785291018028
GO:0010468regulation of gene expression0.0218552790271866
GO:0031323regulation of cellular metabolic process0.026685242233463
GO:0018193peptidyl-amino acid modification0.0288652314441864
GO:0004652polynucleotide adenylyltransferase activity0.0288652314441864
GO:0019222regulation of metabolic process0.0300666077364779
GO:0048505regulation of timing of cell differentiation0.0332166159399697
GO:0040034regulation of development, heterochronic0.0332166159399697
GO:0016486peptide hormone processing0.0430581140249115
GO:0018210peptidyl-threonine modification0.0430581140249115
GO:0018107peptidyl-threonine phosphorylation0.0430581140249115
GO:0001837epithelial to mesenchymal transition0.0480139548102052



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
lymphocyte7.61e-0813
common lymphoid progenitor7.61e-0813
lymphoid lineage restricted progenitor cell8.35e-0812
T cell3.77e-0711
pro-T cell3.77e-0711

Uber Anatomy
Ontology termp-valuen
anterior region of body5.67e-0843
craniocervical region1.40e-0736
respiratory tract1.97e-0741
respiratory system2.68e-0742
hemopoietic organ2.73e-0729
immune organ2.73e-0729
mixed endoderm/mesoderm-derived structure6.56e-0735


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)
MA0003.11.35674
MA0004.10.104042
MA0006.10.321056
MA0007.10.656832
MA0009.10.412602
MA0014.14.27715
MA0017.10.0425137
MA0019.10.268299
MA0024.10.982128
MA0025.10.616209
MA0027.11.99083
MA0028.10.964323
MA0029.10.358857
MA0030.10.364159
MA0031.10.335674
MA0038.10.190128
MA0040.10.423075
MA0041.10.0680579
MA0042.10.224462
MA0043.10.495015
MA0046.10.442826
MA0048.10.366277
MA0050.10.12507
MA0051.10.196084
MA0052.10.429851
MA0055.10.0200406
MA0056.10
MA0057.11.93668
MA0058.10.0597941
MA0059.10.231081
MA0060.10.889814
MA0061.10.229521
MA0063.10
MA0066.10.53876
MA0067.10.717937
MA0068.10.10147
MA0069.10.430137
MA0070.10.421986
MA0071.10.124599
MA0072.10.414891
MA0073.10.00426612
MA0074.10.160032
MA0076.11.11784
MA0077.10.396883
MA0078.10.218627
MA0081.10.936282
MA0083.10.494326
MA0084.11.02883
MA0087.10.457205
MA0088.12.04408
MA0089.10
MA0090.10.0869074
MA0091.10.110977
MA0092.10.29369
MA0093.10.0399156
MA0095.10
MA0098.10
MA0100.10.907524
MA0101.10.519199
MA0103.10.0462215
MA0105.10.52902
MA0106.10.224053
MA0107.10.168906
MA0108.20.285422
MA0109.10
MA0111.10.0938213
MA0113.10.20458
MA0114.10.0900443
MA0115.10.497446
MA0116.10.583641
MA0117.10.469566
MA0119.10.242709
MA0122.10.486676
MA0124.10.668899
MA0125.10.601578
MA0130.10
MA0131.12.07199
MA0132.10
MA0133.10
MA0135.10.526836
MA0136.10.513613
MA0139.10.0490456
MA0140.10.464908
MA0141.10.197414
MA0142.10.324241
MA0143.10.215799
MA0144.10.230788
MA0145.10.114967
MA0146.11.74485
MA0147.10.473869
MA0148.10.112635
MA0149.11.8872
MA0062.21.82797
MA0035.20.155719
MA0039.24.45988
MA0138.20.259078
MA0002.20.139327
MA0137.20.430805
MA0104.20.319656
MA0047.20.18962
MA0112.20.500556
MA0065.20.0546357
MA0150.10.0963127
MA0151.10
MA0152.10.189691
MA0153.10.541494
MA0154.10.212555
MA0155.10.405027
MA0156.10.724462
MA0157.10.299365
MA0158.10
MA0159.10.805512
MA0160.10.114259
MA0161.10
MA0162.12.02296
MA0163.10.554882
MA0164.10.514179
MA0080.20.169853
MA0018.23.04418
MA0099.20.254459
MA0079.25.52854
MA0102.21.07954
MA0258.10.203197
MA0259.10.720568
MA0442.10
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