Personal tools

MCL coexpression mm9:1551: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 7: Line 7:
|ontology_enrichment_uberon=UBERON:0002384!1.54e-14!46;UBERON:0000490!7.92e-08!66;UBERON:0002193!1.24e-07!48;UBERON:0002405!1.24e-07!48;UBERON:0002390!3.17e-07!45;UBERON:0003061!3.17e-07!45
|ontology_enrichment_uberon=UBERON:0002384!1.54e-14!46;UBERON:0000490!7.92e-08!66;UBERON:0002193!1.24e-07!48;UBERON:0002405!1.24e-07!48;UBERON:0002390!3.17e-07!45;UBERON:0003061!3.17e-07!45
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.087078,0.529553,0.603273,0.406364,0.618805,0.715644,0.812379,0.310789,0.115752,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.545768,0.489529,0.145201,0.727684,0.404661,1.32977,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,0.425309,0.20704,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.227872,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,0.152094,1.23259,0.257421,0.686172,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,2.21546,1.1148,0.574099,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,1.7727,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.328405,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,1.77493,1.43666,0.44142,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,1.5287,0.851091,2.18247,0.569503,1.05179,0.230371,0.416978,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,2.28884,0.547782,0.90208,0.741834,0.383572,0.701187,0.425122
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.087078,0.529553,0.603273,0.406364,0.618805,0.715644,0.812379,0.310789,0.115752,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.545768,0.489529,0.145201,0.727684,0.404661,1.32977,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,0.425309,0.20704,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.227872,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,0.152094,1.23259,0.257421,0.686172,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,2.21546,1.1148,0.574099,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,1.7727,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.328405,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,1.77493,1.43666,0.44142,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,1.5287,0.851091,2.18247,0.569503,1.05179,0.230371,0.416978,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,2.28884,0.547782,0.90208,0.741834,0.383572,0.701187,0.425122
|tfbs_overrepresentation_jaspar=MA0003.1;0.0185483,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.0502051,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;1.93142,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;2.23359,MA0042.1;1.26591,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;0.205696,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.28842,MA0056.1;0,MA0057.1;0.192781,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;1.58413,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;1.08757,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;2.09333,MA0074.1;0.708108,MA0076.1;1.1853,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;0.148348,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;0.567278,MA0093.1;0.440484,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;0.248108,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;2.07761,MA0109.1;0,MA0111.1;1.4237,MA0113.1;0.780358,MA0114.1;0.361633,MA0115.1;1.16466,MA0116.1;0.419688,MA0117.1;1.13165,MA0119.1;0.524046,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;0.295945,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.956957,MA0145.1;0.157686,MA0146.1;0.21827,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;2.81639,MA0035.2;0.700704,MA0039.2;0.140205,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;0.315156,MA0047.2;0.75686,MA0112.2;0.157681,MA0065.2;0.158101,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.203217,MA0155.1;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.245828,MA0163.1;0.497328,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.00167664,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}
}}

Revision as of 13:30, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:115885803..115885825,-p2@Gm12657
p2@Gm6421
p2@Gm6749
p2@Gm7194
p2@Gm7227
p2@H3f3a
p2@H3f3b
p2@H3f3c
Mm9::chr17:27666934..27666939,+p1@ENSMUST00000119573
Mm9::chr18:15991281..15991283,+p1@Gm10036
Mm9::chr18:60934280..60934317,+p1@Rps14
Mm9::chrX:69048950..69048954,+p1@ENSMUST00000164796


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:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.03067988823755
GO:0015935small ribosomal subunit0.0328713088259464
GO:0005830cytosolic ribosome (sensu Eukaryota)0.0339670191201446
GO:0033279ribosomal subunit0.0339670191201446
GO:0044445cytosolic part0.0411987070618529
GO:0042254ribosome biogenesis and assembly0.0446501944885772
GO:0003735structural constituent of ribosome0.0446501944885772
GO:0005840ribosome0.0446501944885772
GO:0022613ribonucleoprotein complex biogenesis and assembly0.046019832356325



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
somatic cell8.22e-18118
animal cell1.55e-16115
eukaryotic cell1.55e-16115
motile cell1.53e-1454
connective tissue cell1.54e-1446
mesenchymal cell1.54e-1446
stem cell1.07e-1397
hematopoietic cell1.61e-1332
hematopoietic oligopotent progenitor cell1.61e-1332
hematopoietic stem cell1.61e-1332
angioblastic mesenchymal cell1.61e-1332
hematopoietic multipotent progenitor cell1.61e-1332
somatic stem cell4.56e-1191
multi fate stem cell4.56e-1191
hematopoietic lineage restricted progenitor cell3.34e-1025
lymphoid lineage restricted progenitor cell3.08e-0812
lymphocyte9.38e-0813
common lymphoid progenitor9.38e-0813
T cell1.34e-0711
pro-T cell1.34e-0711
leukocyte1.73e-0717
nongranular leukocyte1.73e-0717
common myeloid progenitor3.91e-0719
nucleate cell7.79e-0716
mature alpha-beta T cell9.98e-079
alpha-beta T cell9.98e-079
immature T cell9.98e-079
mature T cell9.98e-079
immature alpha-beta T cell9.98e-079

Uber Anatomy
Ontology termp-valuen
connective tissue1.54e-1446
unilaminar epithelium7.92e-0866
hemolymphoid system1.24e-0748
immune system1.24e-0748
hematopoietic system3.17e-0745
blood island3.17e-0745


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)
MA0003.10.0185483
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.0502051
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.11.93142
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.12.23359
MA0042.11.26591
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.28842
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.11.58413
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.11.08757
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.12.09333
MA0074.10.708108
MA0076.11.1853
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.22.07761
MA0109.10
MA0111.11.4237
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.956957
MA0145.10.157686
MA0146.10.21827
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.22.81639
MA0035.20.700704
MA0039.20.140205
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.245828
MA0163.10.497328
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.00167664
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:1551&oldid=2574946"