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MCL coexpression mm9:565: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002384!2.91e-12!46;UBERON:0002193!3.16e-08!48;UBERON:0002405!3.16e-08!48;UBERON:0002390!3.35e-08!45;UBERON:0003061!3.35e-08!45
|ontology_enrichment_uberon=UBERON:0002384!2.91e-12!46;UBERON:0002193!3.16e-08!48;UBERON:0002405!3.16e-08!48;UBERON:0002390!3.35e-08!45;UBERON:0003061!3.35e-08!45
|tfbs_overrepresentation_for_novel_motifs=0.684947,0.0867717,0.635766,0.279403,0.138992,0.291576,0.370193,0.268276,0.0833551,0.282547,0.883008,0.35958,0.0780266,0.381063,0.15081,0,0.557619,0.133477,0.069633,0.286444,0.567339,0.383765,1.75669,0.137915,0.229596,0.405649,0.0651848,0.309422,0.511682,0.169823,0.805906,0.653099,0.412165,0.202991,0.900171,0.0120558,0.790102,0.937845,0.111088,0.0929685,0.136186,0.815844,0.0669139,0.152251,0.228983,0.743728,0.48361,0.322976,0.282668,0.517045,0.541299,0.429887,0.160439,0.788877,0.805733,0.387424,0.18067,0.348382,0.218496,0.385607,0.634076,0.438439,0.302747,0.5308,1.81556,1.39513,0.938213,1.28193,0.629645,1.13654,0.208654,0.984639,0.408053,0.838198,0.0571922,0.192403,0.202885,0.473159,0.617814,0.198007,0.587166,1.40622,0.437131,0.548458,0.72691,1.00112,0.0297453,0.170021,1.22406,1.44275,1.0064,0.731688,0.665283,0.143149,0.351307,0.321665,0.264364,0.667958,1.21491,0.938299,0.396021,0.652833,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,1.1054,0.196131,0.671624,0.773781,0.19888,0.336214,1.01331,0.41985,0.037872,0.772215,1.37442,0.389429,0.843435,0.511336,0.407285,0.472327,1.06644,0.621313,0.377415,0.658832,0.936732,0.145259,0.755703,1.37647,0.907893,1.82327,1.03449,0.62534,0.251471,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,0.53483,0.302189,0.486482,1.76978,0.253405,1.98864,0.391484,0.57615,0.790393,0.331601,0.398786,0.869538,0.430798,0.159498,0.680297,0.700333,0.995609,0.726089,1.50676,0.237049,0.531751,0.392164,0.12482,0.941787,0.171655
|tfbs_overrepresentation_for_novel_motifs=0.684947,0.0867717,0.635766,0.279403,0.138992,0.291576,0.370193,0.268276,0.0833551,0.282547,0.883008,0.35958,0.0780266,0.381063,0.15081,0,0.557619,0.133477,0.069633,0.286444,0.567339,0.383765,1.75669,0.137915,0.229596,0.405649,0.0651848,0.309422,0.511682,0.169823,0.805906,0.653099,0.412165,0.202991,0.900171,0.0120558,0.790102,0.937845,0.111088,0.0929685,0.136186,0.815844,0.0669139,0.152251,0.228983,0.743728,0.48361,0.322976,0.282668,0.517045,0.541299,0.429887,0.160439,0.788877,0.805733,0.387424,0.18067,0.348382,0.218496,0.385607,0.634076,0.438439,0.302747,0.5308,1.81556,1.39513,0.938213,1.28193,0.629645,1.13654,0.208654,0.984639,0.408053,0.838198,0.0571922,0.192403,0.202885,0.473159,0.617814,0.198007,0.587166,1.40622,0.437131,0.548458,0.72691,1.00112,0.0297453,0.170021,1.22406,1.44275,1.0064,0.731688,0.665283,0.143149,0.351307,0.321665,0.264364,0.667958,1.21491,0.938299,0.396021,0.652833,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,1.1054,0.196131,0.671624,0.773781,0.19888,0.336214,1.01331,0.41985,0.037872,0.772215,1.37442,0.389429,0.843435,0.511336,0.407285,0.472327,1.06644,0.621313,0.377415,0.658832,0.936732,0.145259,0.755703,1.37647,0.907893,1.82327,1.03449,0.62534,0.251471,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,0.53483,0.302189,0.486482,1.76978,0.253405,1.98864,0.391484,0.57615,0.790393,0.331601,0.398786,0.869538,0.430798,0.159498,0.680297,0.700333,0.995609,0.726089,1.50676,0.237049,0.531751,0.392164,0.12482,0.941787,0.171655
|tfbs_overrepresentation_jaspar=MA0003.1;0.235152,MA0004.1;0.765938,MA0006.1;0.14766,MA0007.1;0.267314,MA0009.1;0.678286,MA0014.1;0.00936227,MA0017.1;0.965594,MA0019.1;0.506787,MA0024.1;0.636635,MA0025.1;0.9035,MA0027.1;2.3071,MA0028.1;7.19605,MA0029.1;0.616052,MA0030.1;0.622264,MA0031.1;0.588678,MA0038.1;1.04584,MA0040.1;0.690239,MA0041.1;0.218039,MA0042.1;0.207696,MA0043.1;0.771094,MA0046.1;0.712646,MA0048.1;0.0358824,MA0050.1;0.312673,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;0.0835619,MA0056.1;0,MA0057.1;0.127633,MA0058.1;1.73925,MA0059.1;1.79197,MA0060.1;1.59086,MA0061.1;0.363764,MA0063.1;0,MA0066.1;0.395746,MA0067.1;1.01206,MA0068.1;0.132828,MA0069.1;0.698271,MA0070.1;1.64714,MA0071.1;0.311956,MA0072.1;0.680902,MA0073.1;0.344781,MA0074.1;0.954464,MA0076.1;7.67934,MA0077.1;0.660245,MA0078.1;0.443468,MA0081.1;1.21585,MA0083.1;0.77033,MA0084.1;1.33532,MA0087.1;0.728855,MA0088.1;0.965806,MA0089.1;0,MA0090.1;0.251458,MA0091.1;0.290854,MA0092.1;0.251716,MA0093.1;0.941822,MA0095.1;0,MA0098.1;0,MA0100.1;0.353762,MA0101.1;1.1726,MA0103.1;0.174916,MA0105.1;0.196316,MA0106.1;0.450539,MA0107.1;0.979629,MA0108.2;0.527977,MA0109.1;0,MA0111.1;0.263095,MA0113.1;0.424958,MA0114.1;0.727901,MA0115.1;0.773793,MA0116.1;0.147513,MA0117.1;0.742722,MA0119.1;0.219527,MA0122.1;0.761823,MA0124.1;0.959967,MA0125.1;0.887718,MA0130.1;0,MA0131.1;1.25498,MA0132.1;0,MA0133.1;0,MA0135.1;0.806261,MA0136.1;1.76101,MA0139.1;0.0756871,MA0140.1;0.353662,MA0141.1;0.18979,MA0142.1;0.575041,MA0143.1;0.439766,MA0144.1;0.365041,MA0145.1;0.0201868,MA0146.1;1.3531,MA0147.1;0.386218,MA0148.1;0.293462,MA0149.1;0.223436,MA0062.2;11.7646,MA0035.2;0.357786,MA0039.2;0.290079,MA0138.2;0.495254,MA0002.2;0.0773396,MA0137.2;0.55008,MA0104.2;0.289861,MA0047.2;0.404891,MA0112.2;0.0201854,MA0065.2;0.0897174,MA0150.1;0.267221,MA0151.1;0,MA0152.1;0.404987,MA0153.1;0.822355,MA0154.1;0.0349712,MA0155.1;0.105935,MA0156.1;2.29993,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.128669,MA0160.1;0.80274,MA0161.1;0,MA0162.1;0.258547,MA0163.1;0.584775,MA0164.1;0.381832,MA0080.2;0.509758,MA0018.2;1.01279,MA0099.2;0.489441,MA0079.2;0.0170765,MA0102.2;1.38728,MA0258.1;0.103004,MA0259.1;0.114734,MA0442.1;0
}}
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Revision as of 11:57, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:97888253..97888282,+p1@LOC100045367
p1@LOC100505098
p1@Rpl19
Mm9::chr12:4824351..4824384,+p1@0610009D07Rik
Mm9::chr13:91062727..91062775,+p1@Gm10186
p1@Gm15450
p1@Rps23
Mm9::chr16:33056542..33056581,+p1@Gm11810
p1@Gm14279
p1@LOC100505045
p1@LOC100505110
p1@Rpl35a-ps7
p1@Rpl35a
Mm9::chr18:60934268..60934279,+p2@Rps14
Mm9::chr1:135506830..135506871,-p1@Snrpe
Mm9::chr3:130433228..130433270,-p1@Gm10086
p1@Gm4705
p1@Rpl34-ps1
p1@Rpl34
Mm9::chr4:135609258..135609330,-p1@Rpl11
Mm9::chr6:8209098..8209153,-p1@Rpa3
Mm9::chr6:86321483..86321544,+p1@Gm8186
p1@Snrpg
Mm9::chr7:125259685..125259712,-p1@Gm10196
p1@Gm14166
p1@Rps15a
Mm9::chr7:52379703..52379724,-p2@Rps11
Mm9::chr8:73197263..73197327,+p1@Lsm4


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:0003723RNA binding2.7068334868066e-07
GO:0030529ribonucleoprotein complex5.39890992168826e-06
GO:0003735structural constituent of ribosome0.000344208073032711
GO:0005840ribosome0.000344208073032711
GO:0008380RNA splicing0.000344208073032711
GO:0019843rRNA binding0.000344208073032711
GO:0010467gene expression0.000477639320630132
GO:0006397mRNA processing0.000477639320630132
GO:0003676nucleic acid binding0.000477639320630132
GO:0016071mRNA metabolic process0.000581313419145666
GO:0005830cytosolic ribosome (sensu Eukaryota)0.000833266362289732
GO:0043170macromolecule metabolic process0.000973998213762906
GO:0006396RNA processing0.0010808190559382
GO:0033279ribosomal subunit0.0010808190559382
GO:0032991macromolecular complex0.0010808190559382
GO:0006412translation0.0016737208799554
GO:0044238primary metabolic process0.00181684662869837
GO:0044237cellular metabolic process0.00181684662869837
GO:0044445cytosolic part0.00185370701054734
GO:0043232intracellular non-membrane-bound organelle0.00340499698575161
GO:0043228non-membrane-bound organelle0.00340499698575161
GO:0005681spliceosome0.00340499698575161
GO:0043229intracellular organelle0.00340499698575161
GO:0043226organelle0.00340499698575161
GO:0009059macromolecule biosynthetic process0.00351279412926422
GO:0044249cellular biosynthetic process0.00741740606131899
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.0082982174934516
GO:0044424intracellular part0.0102785707572212
GO:0031202RNA splicing factor activity, transesterification mechanism0.0102961576755971
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0116079617877804
GO:0005622intracellular0.0116578670353437
GO:0005732small nucleolar ribonucleoprotein complex0.0116578670353437
GO:0044446intracellular organelle part0.0121640679171278
GO:0044422organelle part0.0121640679171278
GO:0005829cytosol0.012466216839066
GO:0009058biosynthetic process0.0126317215802539
GO:0015935small ribosomal subunit0.0201153190906232
GO:0015934large ribosomal subunit0.0208848363598456
GO:0044452nucleolar part0.0228779551165436
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.024978941652727



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
connective tissue2.91e-1246
hemolymphoid system3.16e-0848
immune system3.16e-0848
hematopoietic system3.35e-0845
blood island3.35e-0845


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)
MA0003.10.235152
MA0004.10.765938
MA0006.10.14766
MA0007.10.267314
MA0009.10.678286
MA0014.10.00936227
MA0017.10.965594
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.17.19605
MA0029.10.616052
MA0030.10.622264
MA0031.10.588678
MA0038.11.04584
MA0040.10.690239
MA0041.10.218039
MA0042.10.207696
MA0043.10.771094
MA0046.10.712646
MA0048.10.0358824
MA0050.10.312673
MA0051.10.413609
MA0052.10.697946
MA0055.10.0835619
MA0056.10
MA0057.10.127633
MA0058.11.73925
MA0059.11.79197
MA0060.11.59086
MA0061.10.363764
MA0063.10
MA0066.10.395746
MA0067.11.01206
MA0068.10.132828
MA0069.10.698271
MA0070.11.64714
MA0071.10.311956
MA0072.10.680902
MA0073.10.344781
MA0074.10.954464
MA0076.17.67934
MA0077.10.660245
MA0078.10.443468
MA0081.11.21585
MA0083.10.77033
MA0084.11.33532
MA0087.10.728855
MA0088.10.965806
MA0089.10
MA0090.10.251458
MA0091.10.290854
MA0092.10.251716
MA0093.10.941822
MA0095.10
MA0098.10
MA0100.10.353762
MA0101.11.1726
MA0103.10.174916
MA0105.10.196316
MA0106.10.450539
MA0107.10.979629
MA0108.20.527977
MA0109.10
MA0111.10.263095
MA0113.10.424958
MA0114.10.727901
MA0115.10.773793
MA0116.10.147513
MA0117.10.742722
MA0119.10.219527
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.11.25498
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.11.76101
MA0139.10.0756871
MA0140.10.353662
MA0141.10.18979
MA0142.10.575041
MA0143.10.439766
MA0144.10.365041
MA0145.10.0201868
MA0146.11.3531
MA0147.10.386218
MA0148.10.293462
MA0149.10.223436
MA0062.211.7646
MA0035.20.357786
MA0039.20.290079
MA0138.20.495254
MA0002.20.0773396
MA0137.20.55008
MA0104.20.289861
MA0047.20.404891
MA0112.20.0201854
MA0065.20.0897174
MA0150.10.267221
MA0151.10
MA0152.10.404987
MA0153.10.822355
MA0154.10.0349712
MA0155.10.105935
MA0156.12.29993
MA0157.10.545026
MA0158.10
MA0159.10.128669
MA0160.10.80274
MA0161.10
MA0162.10.258547
MA0163.10.584775
MA0164.10.381832
MA0080.20.509758
MA0018.21.01279
MA0099.20.489441
MA0079.20.0170765
MA0102.21.38728
MA0258.10.103004
MA0259.10.114734
MA0442.10
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