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MCL coexpression mm9:910: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0006543;glutamine catabolic process;0.0188916839156807;14660!GO:0004359;glutaminase activity;0.0188916839156807;14660!GO:0002087;neurological control of breathing;0.0188916839156807;14660!GO:0003016;respiratory system process;0.0188916839156807;14660!GO:0005662;DNA replication factor A complex;0.0188916839156807;19291!GO:0046332;SMAD binding;0.0188916839156807;19291!GO:0030894;replisome;0.0188916839156807;19291!GO:0009065;glutamine family amino acid catabolic process;0.0188916839156807;14660!GO:0043601;nuclear replisome;0.0188916839156807;19291!GO:0043596;nuclear replication fork;0.0188916839156807;19291!GO:0006541;glutamine metabolic process;0.0257543293727709;14660!GO:0003697;single-stranded DNA binding;0.0304989438990855;19291!GO:0003690;double-stranded DNA binding;0.0304989438990855;19291!GO:0005657;replication fork;0.0323609045376041;19291!GO:0009064;glutamine family amino acid metabolic process;0.0353831001632472;14660!GO:0003729;mRNA binding;0.0353831001632472;19291!GO:0009063;amino acid catabolic process;0.047627045670694;14660!GO:0043566;structure-specific DNA binding;0.047627045670694;19291!GO:0016811;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides;0.047627045670694;14660!}}
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catabolic process;0.0188916839156807;14660!GO:0004359;glutaminase activity;0.0188916839156807;14660!GO:0002087;neurological control of breathing;0.0188916839156807;14660!GO:0003016;respiratory system process;0.0188916839156807;14660!GO:0005662;DNA replication factor A complex;0.0188916839156807;19291!GO:0046332;SMAD binding;0.0188916839156807;19291!GO:0030894;replisome;0.0188916839156807;19291!GO:0009065;glutamine family amino acid catabolic process;0.0188916839156807;14660!GO:0043601;nuclear replisome;0.0188916839156807;19291!GO:0043596;nuclear replication fork;0.0188916839156807;19291!GO:0006541;glutamine metabolic process;0.0257543293727709;14660!GO:0003697;single-stranded DNA binding;0.0304989438990855;19291!GO:0003690;double-stranded DNA binding;0.0304989438990855;19291!GO:0005657;replication fork;0.0323609045376041;19291!GO:0009064;glutamine family amino acid metabolic process;0.0353831001632472;14660!GO:0003729;mRNA binding;0.0353831001632472;19291!GO:0009063;amino acid catabolic process;0.047627045670694;14660!GO:0043566;structure-specific DNA binding;0.047627045670694;19291!GO:0016811;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides;0.047627045670694;14660!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000073!1.80e-15!54;UBERON:0001049!2.82e-14!52;UBERON:0005068!2.82e-14!52;UBERON:0006241!2.82e-14!52;UBERON:0007135!2.82e-14!52;UBERON:0001017!3.27e-14!73;UBERON:0001016!4.08e-14!75;UBERON:0000955!2.21e-12!47;UBERON:0006238!2.21e-12!47;UBERON:0004121!5.15e-12!95;UBERON:0000924!5.15e-12!95;UBERON:0006601!5.15e-12!95;UBERON:0002616!8.45e-12!46;UBERON:0010371!1.43e-11!73;UBERON:0002346!2.80e-11!64;UBERON:0003075!2.80e-11!64;UBERON:0007284!2.80e-11!64;UBERON:0003080!5.86e-11!40;UBERON:0002780!1.97e-10!39;UBERON:0001890!1.97e-10!39;UBERON:0006240!1.97e-10!39;UBERON:0002020!4.32e-09!34;UBERON:0000064!8.17e-09!99;UBERON:0003056!9.07e-09!49;UBERON:0002021!2.71e-08!10;UBERON:0000411!2.71e-08!10;UBERON:0001950!2.71e-08!10;UBERON:0003528!2.74e-07!29;UBERON:0002791!2.74e-07!29;UBERON:0001893!2.74e-07!29|tfbs_overrepresentation_for_novel_motifs=0.393008,0.84953,0.367606,0.434198,0.260188,0.448401,0.538088,0.515265,0.181564,0.386846,0.494602,0.526159,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.29826,0.883862,0.223663,0.549359,0.717658,0.374936,0.577606,0.153291,0.469052,0.303071,0.376624,1.15331,0.843667,1.29258,0.425071,0.757987,0.185086,1.26012,1.29755,0.221921,0.195877,0.256422,1.16427,0.0558565,0.27776,0.663502,0.423266,0.662995,0.484612,0.170971,0.305876,0.725127,0.604356,0.732634,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,1.31587,1.03623,0.853709,0.131016,0.136938,1.56933,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,1.56717,0.123242,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.1711,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,1.20804,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.603195,1.11602,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.829188,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,1.25168,0.780212,0.986833,1.12835,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.842217|tfbs_overrepresentation_jaspar=MA0003.1;3.09165,MA0004.1;0.434673,MA0006.1;1.37063,MA0007.1;1.07722,MA0009.1;0.870101,MA0014.1;1.54572,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.769859,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.685543,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.117901,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.224905,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.0965831,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.138438,MA0074.1;0.531046,MA0076.1;1.52758,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.980744,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.229377,MA0089.1;0,MA0090.1;0.401197,MA0091.1;1.13691,MA0092.1;0.401504,MA0093.1;0.787675,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;1.33477,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;1.69252,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.633896,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;2.15835,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.977634,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.527241,MA0146.1;1.31232,MA0147.1;0.666991,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;3.38762,MA0035.2;0.524137,MA0039.2;1.07211,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.527225,MA0065.2;0.528619,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;0.0804339,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;4.72045,MA0163.1;0.408151,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;1.37842,MA0099.2;0.669311,MA0079.2;2.0883,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.643936,MA0442.1;0}}

Latest revision as of 16:05, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:6375884..6375920,-p2@Purb
Mm9::chr11:74986055..74986071,+p1@ENSMUST00000134252
Mm9::chr14:70480962..70480969,+p@chr14:70480962..70480969
+
Mm9::chr15:101105031..101105041,+p@chr15:101105031..101105041
+
Mm9::chr1:36996339..36996348,-p5@Tmem131
Mm9::chr1:52289825..52289842,-p6@Gls
Mm9::chr4:86503216..86503253,-p2@Gm13654
p2@LOC639593
p2@Rps6
Mm9::chr5:150438847..150438866,-p2@Hsph1


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:0006543glutamine catabolic process0.0188916839156807
GO:0004359glutaminase activity0.0188916839156807
GO:0002087neurological control of breathing0.0188916839156807
GO:0003016respiratory system process0.0188916839156807
GO:0005662DNA replication factor A complex0.0188916839156807
GO:0046332SMAD binding0.0188916839156807
GO:0030894replisome0.0188916839156807
GO:0009065glutamine family amino acid catabolic process0.0188916839156807
GO:0043601nuclear replisome0.0188916839156807
GO:0043596nuclear replication fork0.0188916839156807
GO:0006541glutamine metabolic process0.0257543293727709
GO:0003697single-stranded DNA binding0.0304989438990855
GO:0003690double-stranded DNA binding0.0304989438990855
GO:0005657replication fork0.0323609045376041
GO:0009064glutamine family amino acid metabolic process0.0353831001632472
GO:0003729mRNA binding0.0353831001632472
GO:0009063amino acid catabolic process0.047627045670694
GO:0043566structure-specific DNA binding0.047627045670694
GO:0016811hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides0.047627045670694



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.80e-1554
neural tube2.82e-1452
neural rod2.82e-1452
future spinal cord2.82e-1452
neural keel2.82e-1452
central nervous system3.27e-1473
nervous system4.08e-1475
brain2.21e-1247
future brain2.21e-1247
ectoderm-derived structure5.15e-1295
ectoderm5.15e-1295
presumptive ectoderm5.15e-1295
regional part of brain8.45e-1246
ecto-epithelium1.43e-1173
neurectoderm2.80e-1164
neural plate2.80e-1164
presumptive neural plate2.80e-1164
anterior neural tube5.86e-1140
regional part of forebrain1.97e-1039
forebrain1.97e-1039
future forebrain1.97e-1039
gray matter4.32e-0934
organ part8.17e-0999
pre-chordal neural plate9.07e-0949
occipital lobe2.71e-0810
visual cortex2.71e-0810
neocortex2.71e-0810
brain grey matter2.74e-0729
regional part of telencephalon2.74e-0729
telencephalon2.74e-0729


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)
MA0003.13.09165
MA0004.10.434673
MA0006.11.37063
MA0007.11.07722
MA0009.10.870101
MA0014.11.54572
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.685543
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.117901
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.138438
MA0074.10.531046
MA0076.11.52758
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
MA0089.10
MA0090.10.401197
MA0091.11.13691
MA0092.10.401504
MA0093.10.787675
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.11.33477
MA0106.10.626997
MA0107.10.301222
MA0108.21.69252
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.633896
MA0115.10.969632
MA0116.10.27152
MA0117.12.15835
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.977634
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.527241
MA0146.11.31232
MA0147.10.666991
MA0148.10.450593
MA0149.10.367458
MA0062.23.38762
MA0035.20.524137
MA0039.21.07211
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.20.527225
MA0065.20.528619
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.0804339
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.14.72045
MA0163.10.408151
MA0164.10.551114
MA0080.20.302064
MA0018.21.37842
MA0099.20.669311
MA0079.22.0883
MA0102.21.59466
MA0258.10.210437
MA0259.10.643936
MA0442.10
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