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MCL coexpression mm9:458: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002384!1.01e-19!46;UBERON:0002193!8.36e-16!48;UBERON:0002405!8.36e-16!48;UBERON:0002390!5.82e-13!45;UBERON:0003061!5.82e-13!45;UBERON:0002370!6.28e-12!23;UBERON:0000974!6.28e-12!23;UBERON:0004807!6.28e-12!23;UBERON:0005058!6.28e-12!23;UBERON:0003351!6.28e-12!23;UBERON:0009113!6.28e-12!23;UBERON:0003295!6.28e-12!23;UBERON:0009722!6.28e-12!23;UBERON:0005562!6.28e-12!23;UBERON:0007690!6.28e-12!23;UBERON:0006562!2.33e-11!24;UBERON:0003408!2.33e-11!24;UBERON:0001557!2.33e-11!24;UBERON:0001042!2.33e-11!24;UBERON:0008814!2.33e-11!24;UBERON:0009145!2.33e-11!24;UBERON:0004177!4.56e-11!29;UBERON:0005057!4.56e-11!29;UBERON:0000072!6.62e-10!27;UBERON:0000077!7.86e-09!35;UBERON:0000063!2.98e-07!35;UBERON:0007811!5.28e-07!36
|ontology_enrichment_uberon=UBERON:0002384!1.01e-19!46;UBERON:0002193!8.36e-16!48;UBERON:0002405!8.36e-16!48;UBERON:0002390!5.82e-13!45;UBERON:0003061!5.82e-13!45;UBERON:0002370!6.28e-12!23;UBERON:0000974!6.28e-12!23;UBERON:0004807!6.28e-12!23;UBERON:0005058!6.28e-12!23;UBERON:0003351!6.28e-12!23;UBERON:0009113!6.28e-12!23;UBERON:0003295!6.28e-12!23;UBERON:0009722!6.28e-12!23;UBERON:0005562!6.28e-12!23;UBERON:0007690!6.28e-12!23;UBERON:0006562!2.33e-11!24;UBERON:0003408!2.33e-11!24;UBERON:0001557!2.33e-11!24;UBERON:0001042!2.33e-11!24;UBERON:0008814!2.33e-11!24;UBERON:0009145!2.33e-11!24;UBERON:0004177!4.56e-11!29;UBERON:0005057!4.56e-11!29;UBERON:0000072!6.62e-10!27;UBERON:0000077!7.86e-09!35;UBERON:0000063!2.98e-07!35;UBERON:0007811!5.28e-07!36
|tfbs_overrepresentation_for_novel_motifs=0.19013,0.0414522,0.510781,0.221468,0.0986112,0.656813,0.305009,0.186307,0.439801,0.0241551,0.742008,0.295134,0.186621,0.315149,0.351364,0,0.482714,0.645746,0.379612,0.89761,0.146132,0.659668,0.3144,0.322638,0.176763,0.338177,1.00403,0.248835,0.126301,0.78695,0.237846,0.574932,0.309242,0.314034,0.714678,0.0161089,0.0875334,0.292182,0.262298,0.221026,0.318773,0.241862,0.599247,0.354562,0.510293,0.610939,0.41191,0.26128,0.491562,0.128181,0.467043,0.360991,0.466115,0.7073,0.723811,0.321095,0.417292,0.284741,0.338309,0.319396,0.556492,0.369066,0.469805,0.456979,0.330403,0.493315,0.854035,1.19441,0.552202,1.05011,0.158281,0.754696,0.453542,0.755651,0.322986,0.546831,0.313869,1.03797,0.540754,0.148967,0.433876,0.498379,0.36783,1.091,0.646739,0.0340059,1.00531,0.262344,0.416206,1.35441,0.92132,0.6514,0.586758,0.102076,0.073664,0.49924,0.409982,2.45335,0.412133,0.416704,0.295113,0.574674,0.690844,0.467576,1.17798,0.241519,0.52055,0.25809,0.152257,0.147333,0.543885,1.65447,0.457145,0.273484,0.928143,0.0952498,0.402998,0.224335,1.21499,0.289365,0.760792,0.438354,0.339713,0.40118,0.980682,0.544138,1.51588,0.580495,0.852575,0.339019,0.67485,0.617809,0.824167,0.332514,0.949083,0.238175,1.08375,0.681128,0.901468,1.71991,1.32292,0.85857,0.349901,0.584599,0.46084,0.242215,0.414644,1.68046,0.198013,0.672242,0.267549,0.0338738,0.708784,0.514688,0.331737,0.786435,1.69282,0.370626,0.188342,0.570508,0.910663,0.645939,0.544546,0.539942,0.457889,0.869172,0.293289,0.797827,0.0365208
|tfbs_overrepresentation_for_novel_motifs=0.19013,0.0414522,0.510781,0.221468,0.0986112,0.656813,0.305009,0.186307,0.439801,0.0241551,0.742008,0.295134,0.186621,0.315149,0.351364,0,0.482714,0.645746,0.379612,0.89761,0.146132,0.659668,0.3144,0.322638,0.176763,0.338177,1.00403,0.248835,0.126301,0.78695,0.237846,0.574932,0.309242,0.314034,0.714678,0.0161089,0.0875334,0.292182,0.262298,0.221026,0.318773,0.241862,0.599247,0.354562,0.510293,0.610939,0.41191,0.26128,0.491562,0.128181,0.467043,0.360991,0.466115,0.7073,0.723811,0.321095,0.417292,0.284741,0.338309,0.319396,0.556492,0.369066,0.469805,0.456979,0.330403,0.493315,0.854035,1.19441,0.552202,1.05011,0.158281,0.754696,0.453542,0.755651,0.322986,0.546831,0.313869,1.03797,0.540754,0.148967,0.433876,0.498379,0.36783,1.091,0.646739,0.0340059,1.00531,0.262344,0.416206,1.35441,0.92132,0.6514,0.586758,0.102076,0.073664,0.49924,0.409982,2.45335,0.412133,0.416704,0.295113,0.574674,0.690844,0.467576,1.17798,0.241519,0.52055,0.25809,0.152257,0.147333,0.543885,1.65447,0.457145,0.273484,0.928143,0.0952498,0.402998,0.224335,1.21499,0.289365,0.760792,0.438354,0.339713,0.40118,0.980682,0.544138,1.51588,0.580495,0.852575,0.339019,0.67485,0.617809,0.824167,0.332514,0.949083,0.238175,1.08375,0.681128,0.901468,1.71991,1.32292,0.85857,0.349901,0.584599,0.46084,0.242215,0.414644,1.68046,0.198013,0.672242,0.267549,0.0338738,0.708784,0.514688,0.331737,0.786435,1.69282,0.370626,0.188342,0.570508,0.910663,0.645939,0.544546,0.539942,0.457889,0.869172,0.293289,0.797827,0.0365208
|tfbs_overrepresentation_jaspar=MA0003.1;0.650281,MA0004.1;0.221835,MA0006.1;0.344361,MA0007.1;0.210531,MA0009.1;0.599391,MA0014.1;0.0349468,MA0017.1;0.774877,MA0019.1;1.94031,MA0024.1;0.558971,MA0025.1;0.819843,MA0027.1;2.21717,MA0028.1;0.360944,MA0029.1;0.53905,MA0030.1;0.545058,MA0031.1;0.512616,MA0038.1;0.33811,MA0040.1;0.611015,MA0041.1;0.166538,MA0042.1;0.476352,MA0043.1;0.689898,MA0046.1;0.632833,MA0048.1;0.420794,MA0050.1;0.701661,MA0051.1;0.914027,MA0052.1;0.618515,MA0055.1;0.71373,MA0056.1;0,MA0057.1;0.0166073,MA0058.1;0.152805,MA0059.1;0.161227,MA0060.1;0.0623353,MA0061.1;1.42881,MA0063.1;0,MA0066.1;0.328887,MA0067.1;0.92691,MA0068.1;0.394673,MA0069.1;0.618831,MA0070.1;0.609808,MA0071.1;0.251158,MA0072.1;0.601934,MA0073.1;0.64502,MA0074.1;0.8099,MA0076.1;0.418364,MA0077.1;0.581866,MA0078.1;0.37382,MA0081.1;1.00846,MA0083.1;0.68915,MA0084.1;1.24749,MA0087.1;0.648637,MA0088.1;0.251567,MA0089.1;0,MA0090.1;0.196267,MA0091.1;0.655274,MA0092.1;0.571528,MA0093.1;0.11723,MA0095.1;0,MA0098.1;0,MA0100.1;0.289731,MA0101.1;0.501038,MA0103.1;0.805091,MA0105.1;0.556586,MA0106.1;0.380511,MA0107.1;0.394565,MA0108.2;0.454274,MA0109.1;0,MA0111.1;0.206727,MA0113.1;0.937714,MA0114.1;0.263654,MA0115.1;0.692537,MA0116.1;0.700593,MA0117.1;0.662171,MA0119.1;0.16785,MA0122.1;0.680832,MA0124.1;0.875485,MA0125.1;0.804312,MA0130.1;0,MA0131.1;0.43,MA0132.1;0,MA0133.1;0,MA0135.1;0.724328,MA0136.1;0.84684,MA0139.1;1.10408,MA0140.1;0.788302,MA0141.1;0.141822,MA0142.1;0.499475,MA0143.1;0.37032,MA0144.1;0.0778672,MA0145.1;0.732278,MA0146.1;0.479142,MA0147.1;0.286569,MA0148.1;1.23068,MA0149.1;0.171305,MA0062.2;0.315856,MA0035.2;1.45004,MA0039.2;0.0201111,MA0138.2;0.423003,MA0002.2;0.728364,MA0137.2;0.139909,MA0104.2;0.204256,MA0047.2;0.895806,MA0112.2;0.00977202,MA0065.2;0.278863,MA0150.1;0.604793,MA0151.1;0,MA0152.1;0.337555,MA0153.1;0.740107,MA0154.1;1.00102,MA0155.1;0.54521,MA0156.1;1.3383,MA0157.1;0.47062,MA0158.1;0,MA0159.1;0.0900717,MA0160.1;0.23657,MA0161.1;0,MA0162.1;0.138028,MA0163.1;0.517288,MA0164.1;2.32847,MA0080.2;0.790324,MA0018.2;1.55937,MA0099.2;0.417463,MA0079.2;0.0832388,MA0102.2;1.29919,MA0258.1;0.0692929,MA0259.1;0.0787033,MA0442.1;0
}}
}}

Revision as of 11:47, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:95861417..95861427,+p@chr10:95861417..95861427
+
Mm9::chr13:51862932..51862937,-p@chr13:51862932..51862937
-
Mm9::chr14:70174964..70175000,+p@chr14:70174964..70175000
+
Mm9::chr15:81997354..81997363,-p@chr15:81997354..81997363
-
Mm9::chr17:31204294..31204303,+p@chr17:31204294..31204303
+
Mm9::chr18:49915420..49915439,+p1@ENSMUST00000149935
p1@uc008ewm.1
Mm9::chr19:57191894..57191911,+p@chr19:57191894..57191911
+
Mm9::chr1:179188927..179188939,+p@chr1:179188927..179188939
+
Mm9::chr1:55188467..55188498,-p@chr1:55188467..55188498
-
Mm9::chr1:66109380..66109430,+p2@ENSMUST00000118496
Mm9::chr3:87945548..87945561,-p@chr3:87945548..87945561
-
Mm9::chr5:66252597..66252607,+p7@Rhoh
Mm9::chr6:22280831..22280835,+p@chr6:22280831..22280835
+
Mm9::chr8:26213486..26213502,-p@chr8:26213486..26213502
-
Mm9::chrX:104284681..104284722,+p1@P2ry10
Mm9::chrX:104284725..104284748,+p2@P2ry10


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:0045028purinergic nucleotide receptor activity, G-protein coupled0.0295558126620671
GO:0001608nucleotide receptor activity, G-protein coupled0.0295558126620671
GO:0016502nucleotide receptor activity0.0295558126620671
GO:0001614purinergic nucleotide receptor activity0.0295558126620671



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
lymphoid lineage restricted progenitor cell1.01e-3112
hematopoietic cell5.95e-3032
hematopoietic oligopotent progenitor cell5.95e-3032
hematopoietic stem cell5.95e-3032
angioblastic mesenchymal cell5.95e-3032
hematopoietic multipotent progenitor cell5.95e-3032
lymphocyte4.00e-2913
common lymphoid progenitor4.00e-2913
mature alpha-beta T cell7.65e-299
alpha-beta T cell7.65e-299
immature T cell7.65e-299
mature T cell7.65e-299
immature alpha-beta T cell7.65e-299
T cell2.24e-2811
pro-T cell2.24e-2811
CD4-positive, alpha-beta T cell1.57e-258
hematopoietic lineage restricted progenitor cell1.26e-2325
nucleate cell2.84e-2316
leukocyte8.80e-2217
nongranular leukocyte8.80e-2217
connective tissue cell1.01e-1946
mesenchymal cell1.01e-1946
thymocyte5.95e-196
double negative thymocyte5.95e-196
naive T cell5.95e-196
double-positive, alpha-beta thymocyte5.95e-196
CD4-positive, alpha-beta thymocyte5.95e-196
naive thymus-derived CD4-positive, alpha-beta T cell5.95e-196
DN4 thymocyte5.95e-196
DN1 thymic pro-T cell5.95e-196
DN2 thymocyte5.95e-196
DN3 thymocyte5.95e-196
immature single positive thymocyte5.95e-196
early T lineage precursor5.95e-196
mature CD4 single-positive thymocyte5.95e-196
resting double-positive thymocyte5.95e-196
double-positive blast5.95e-196
CD69-positive double-positive thymocyte5.95e-196
CD69-positive, CD4-positive single-positive thymocyte5.95e-196
CD4-positive, CD8-intermediate double-positive thymocyte5.95e-196
CD24-positive, CD4 single-positive thymocyte5.95e-196
motile cell2.98e-1654
stem cell5.98e-1197
somatic stem cell3.80e-0891
multi fate stem cell3.80e-0891
common myeloid progenitor1.49e-0719

Uber Anatomy
Ontology termp-valuen
connective tissue1.01e-1946
hemolymphoid system8.36e-1648
immune system8.36e-1648
hematopoietic system5.82e-1345
blood island5.82e-1345
thymus6.28e-1223
neck6.28e-1223
respiratory system epithelium6.28e-1223
hemolymphoid system gland6.28e-1223
pharyngeal epithelium6.28e-1223
thymic region6.28e-1223
pharyngeal gland6.28e-1223
entire pharyngeal arch endoderm6.28e-1223
thymus primordium6.28e-1223
early pharyngeal endoderm6.28e-1223
pharynx2.33e-1124
gland of gut2.33e-1124
upper respiratory tract2.33e-1124
chordate pharynx2.33e-1124
pharyngeal arch system2.33e-1124
pharyngeal region of foregut2.33e-1124
hemopoietic organ4.56e-1129
immune organ4.56e-1129
segment of respiratory tract6.62e-1027
mixed endoderm/mesoderm-derived structure7.86e-0935
organ segment2.98e-0735
craniocervical region5.28e-0736


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)
MA0003.10.650281
MA0004.10.221835
MA0006.10.344361
MA0007.10.210531
MA0009.10.599391
MA0014.10.0349468
MA0017.10.774877
MA0019.11.94031
MA0024.10.558971
MA0025.10.819843
MA0027.12.21717
MA0028.10.360944
MA0029.10.53905
MA0030.10.545058
MA0031.10.512616
MA0038.10.33811
MA0040.10.611015
MA0041.10.166538
MA0042.10.476352
MA0043.10.689898
MA0046.10.632833
MA0048.10.420794
MA0050.10.701661
MA0051.10.914027
MA0052.10.618515
MA0055.10.71373
MA0056.10
MA0057.10.0166073
MA0058.10.152805
MA0059.10.161227
MA0060.10.0623353
MA0061.11.42881
MA0063.10
MA0066.10.328887
MA0067.10.92691
MA0068.10.394673
MA0069.10.618831
MA0070.10.609808
MA0071.10.251158
MA0072.10.601934
MA0073.10.64502
MA0074.10.8099
MA0076.10.418364
MA0077.10.581866
MA0078.10.37382
MA0081.11.00846
MA0083.10.68915
MA0084.11.24749
MA0087.10.648637
MA0088.10.251567
MA0089.10
MA0090.10.196267
MA0091.10.655274
MA0092.10.571528
MA0093.10.11723
MA0095.10
MA0098.10
MA0100.10.289731
MA0101.10.501038
MA0103.10.805091
MA0105.10.556586
MA0106.10.380511
MA0107.10.394565
MA0108.20.454274
MA0109.10
MA0111.10.206727
MA0113.10.937714
MA0114.10.263654
MA0115.10.692537
MA0116.10.700593
MA0117.10.662171
MA0119.10.16785
MA0122.10.680832
MA0124.10.875485
MA0125.10.804312
MA0130.10
MA0131.10.43
MA0132.10
MA0133.10
MA0135.10.724328
MA0136.10.84684
MA0139.11.10408
MA0140.10.788302
MA0141.10.141822
MA0142.10.499475
MA0143.10.37032
MA0144.10.0778672
MA0145.10.732278
MA0146.10.479142
MA0147.10.286569
MA0148.11.23068
MA0149.10.171305
MA0062.20.315856
MA0035.21.45004
MA0039.20.0201111
MA0138.20.423003
MA0002.20.728364
MA0137.20.139909
MA0104.20.204256
MA0047.20.895806
MA0112.20.00977202
MA0065.20.278863
MA0150.10.604793
MA0151.10
MA0152.10.337555
MA0153.10.740107
MA0154.11.00102
MA0155.10.54521
MA0156.11.3383
MA0157.10.47062
MA0158.10
MA0159.10.0900717
MA0160.10.23657
MA0161.10
MA0162.10.138028
MA0163.10.517288
MA0164.12.32847
MA0080.20.790324
MA0018.21.55937
MA0099.20.417463
MA0079.20.0832388
MA0102.21.29919
MA0258.10.0692929
MA0259.10.0787033
MA0442.10
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