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MCL coexpression mm9:2175: Difference between revisions

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{{MCL_coexpression_mm9
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stem cell maintenance;0.0332110056214622;244349!GO:0048864;stem cell development;0.0332110056214622;244349!GO:0019827;stem cell maintenance;0.0332110056214622;244349!GO:0035162;embryonic hemopoiesis;0.0332110056214622;244349!GO:0048863;stem cell differentiation;0.0332110056214622;244349!GO:0000079;regulation of cyclin-dependent protein kinase activity;0.0332110056214622;72949!GO:0006355;regulation of transcription, DNA-dependent;0.0332110056214622;244349,69188,72949!GO:0006351;transcription, DNA-dependent;0.0332110056214622;244349,69188,72949!GO:0032774;RNA biosynthetic process;0.0332110056214622;244349,69188,72949!GO:0004468;lysine N-acetyltransferase activity;0.0332110056214622;244349!GO:0004402;histone acetyltransferase activity;0.0332110056214622;244349!GO:0045449;regulation of transcription;0.0332110056214622;244349,69188,72949!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0332110056214622;244349,69188,72949!GO:0006350;transcription;0.0332110056214622;244349,69188,72949!GO:0016538;cyclin-dependent protein kinase regulator activity;0.0332110056214622;72949!GO:0010468;regulation of gene expression;0.0332110056214622;244349,69188,72949!GO:0031323;regulation of cellular metabolic process;0.0334140566538751;244349,69188,72949!GO:0000910;cytokinesis;0.0334140566538751;72949!GO:0019222;regulation of metabolic process;0.0349312129114998;244349,69188,72949!GO:0016070;RNA metabolic process;0.0357907590948768;244349,69188,72949!GO:0048568;embryonic organ development;0.0423463223766583;244349!GO:0008080;N-acetyltransferase 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|gostat_on_MCL_coexpression=GO:0035019;somatic stem cell maintenance;0.0332110056214622;244349!GO:0048864;stem cell development;0.0332110056214622;244349!GO:0019827;stem cell maintenance;0.0332110056214622;244349!GO:0035162;embryonic hemopoiesis;0.0332110056214622;244349!GO:0048863;stem cell differentiation;0.0332110056214622;244349!GO:0000079;regulation of cyclin-dependent protein kinase activity;0.0332110056214622;72949!GO:0006355;regulation of transcription, DNA-dependent;0.0332110056214622;244349,69188,72949!GO:0006351;transcription, DNA-dependent;0.0332110056214622;244349,69188,72949!GO:0032774;RNA biosynthetic process;0.0332110056214622;244349,69188,72949!GO:0004468;lysine N-acetyltransferase activity;0.0332110056214622;244349!GO:0004402;histone acetyltransferase activity;0.0332110056214622;244349!GO:0045449;regulation of transcription;0.0332110056214622;244349,69188,72949!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0332110056214622;244349,69188,72949!GO:0006350;transcription;0.0332110056214622;244349,69188,72949!GO:0016538;cyclin-dependent protein kinase regulator activity;0.0332110056214622;72949!GO:0010468;regulation of gene expression;0.0332110056214622;244349,69188,72949!GO:0031323;regulation of cellular metabolic process;0.0334140566538751;244349,69188,72949!GO:0000910;cytokinesis;0.0334140566538751;72949!GO:0019222;regulation of metabolic process;0.0349312129114998;244349,69188,72949!GO:0016070;RNA metabolic process;0.0357907590948768;244349,69188,72949!GO:0048568;embryonic organ development;0.0423463223766583;244349!GO:0008080;N-acetyltransferase activity;0.0491289470718693;244349!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000153!3.14e-09!43;UBERON:0007811!1.77e-08!36;UBERON:0001004!7.41e-08!42;UBERON:0000065!1.31e-07!41
|tfbs_overrepresentation_for_novel_motifs=1.54788,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.949265,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.24402,0.570433,0.197567,1.90943,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.318879,1.2563,0.089443,1.16474,0.786577,0.434783,1.03515,0.478558,0.717547,0.544696,0.504971,0.325217,1.61988,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,1.44172,0.377213,0.593145,1.32691,0.323563,0.834514,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,1.80842,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,1.09896,0.409166,0.367176,1.14445,0.938512,0.264911,1.16494,1.12793,1.25667,1.00472,1.00361,1.70541,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.442329,1.65428,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,1.63788,1.27621,1.069,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,1.47798
}}

Latest revision as of 18:07, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:32914180..32914224,+p1@Lrch3
Mm9::chr1:129670760..129670815,+p1@Ccnt2
Mm9::chr5:22940253..22940289,+p1@Mll5
Mm9::chr8:23970000..23970026,+p1@Myst3


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:0035019somatic stem cell maintenance0.0332110056214622
GO:0048864stem cell development0.0332110056214622
GO:0019827stem cell maintenance0.0332110056214622
GO:0035162embryonic hemopoiesis0.0332110056214622
GO:0048863stem cell differentiation0.0332110056214622
GO:0000079regulation of cyclin-dependent protein kinase activity0.0332110056214622
GO:0006355regulation of transcription, DNA-dependent0.0332110056214622
GO:0006351transcription, DNA-dependent0.0332110056214622
GO:0032774RNA biosynthetic process0.0332110056214622
GO:0004468lysine N-acetyltransferase activity0.0332110056214622
GO:0004402histone acetyltransferase activity0.0332110056214622
GO:0045449regulation of transcription0.0332110056214622
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0332110056214622
GO:0006350transcription0.0332110056214622
GO:0016538cyclin-dependent protein kinase regulator activity0.0332110056214622
GO:0010468regulation of gene expression0.0332110056214622
GO:0031323regulation of cellular metabolic process0.0334140566538751
GO:0000910cytokinesis0.0334140566538751
GO:0019222regulation of metabolic process0.0349312129114998
GO:0016070RNA metabolic process0.0357907590948768
GO:0048568embryonic organ development0.0423463223766583
GO:0008080N-acetyltransferase activity0.0491289470718693



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
anterior region of body3.14e-0943
craniocervical region1.77e-0836
respiratory system7.41e-0842
respiratory tract1.31e-0741


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)
MA0003.11.34944
MA0004.10.6888
MA0006.11.24418
MA0007.12.71944
MA0009.11.15569
MA0014.12.62764
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.11.26991
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.735223
MA0050.11.73541
MA0051.10.856094
MA0052.11.17701
MA0055.11.28762
MA0056.10
MA0057.10.701847
MA0058.11.4226
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0471131
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.73268
MA0089.10
MA0090.10.650768
MA0091.11.67688
MA0092.10.651119
MA0093.11.29026
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.11.14526
MA0146.12.17792
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.22.41467
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.211985
MA0065.21.14711
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.13.72407
MA0163.11.11502
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.27.90186
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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