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MCL coexpression mm9:895: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!4.75e-16!118;UBERON:0000925!4.75e-16!118;UBERON:0006595!4.75e-16!118;UBERON:0001007!9.46e-16!116;UBERON:0001555!9.46e-16!116;UBERON:0007026!9.46e-16!116;UBERON:0004921!6.85e-15!114;UBERON:0005409!3.05e-10!47;UBERON:0000077!5.19e-09!35;UBERON:0000160!1.18e-08!31;UBERON:0004923!3.40e-08!24;UBERON:0004177!5.88e-08!29;UBERON:0005057!5.88e-08!29;UBERON:0005911!1.37e-07!69;UBERON:0002193!3.43e-07!48;UBERON:0002405!3.43e-07!48;UBERON:0001004!8.17e-07!42
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.534222,0.367606,0.434198,0.260188,0.448401,0.538088,0.173246,0.181564,0.170907,0.494602,0.526159,0.992329,0.550255,0.756943,0,0.742571,0.252772,0.938682,0.29826,0.883862,0.223663,1.35437,0.258745,0.374936,0.577606,0.466037,0.469052,0.818708,0.376624,0.455168,0.843667,0.250677,0.136998,0.757987,0.60397,0.678971,0.522578,0.221921,0.570041,0.256422,0.460258,0.450632,0.27776,0.403938,0.423266,0.662995,0.484612,0.170971,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.178433,1.31587,1.03623,0.433216,0.131016,0.42492,0.651651,0.806481,0.892913,0.179489,0.759925,0.612313,0.167672,0.920903,2.55025,0.540827,1.23935,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.62322,0.202284,0.510015,0.859272,0.663249,0.332938,0.242106,0.843387,0.967837,0.725721,0.724668,1.16334,0.784351,1.20804,0.903338,0.333829,0.386136,0.96962,0.337254,1.24884,1.21576,0.254749,0.603195,0.437894,0.743872,1.24715,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.479867,0.401212,1.16726,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.766041,0.447587,0.986833,0.598134,0.569994,1.06851,0.605358,0.287226,0.39061,1.03572,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.842217
}}

Latest revision as of 16:03, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:29072948..29072996,+p1@Smek2
Mm9::chr13:104710588..104710652,-p3@Erbb2ip
Mm9::chr14:73725580..73725643,-p1@Rb1
Mm9::chr16:11176363..11176458,-p1@Zc3h7a
Mm9::chr19:7369884..7369958,-p2@Mark2
Mm9::chr3:75360711..75360793,-p1@Pdcd10
Mm9::chr7:135883985..135884039,-p1@Mcmbp
Mm9::chr9:65756774..65756826,+p2@Csnk1g1


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:0045180basal cortex0.0498384313527205
GO:0045651positive regulation of macrophage differentiation0.0498384313527205
GO:0045649regulation of macrophage differentiation0.0498384313527205
GO:0043353enucleate erythrocyte differentiation0.0498384313527205



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 cell7.94e-0712

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.75e-16118
endoderm4.75e-16118
presumptive endoderm4.75e-16118
digestive system9.46e-16116
digestive tract9.46e-16116
primitive gut9.46e-16116
subdivision of digestive tract6.85e-15114
gastrointestinal system3.05e-1047
mixed endoderm/mesoderm-derived structure5.19e-0935
intestine1.18e-0831
organ component layer3.40e-0824
hemopoietic organ5.88e-0829
immune organ5.88e-0829
endo-epithelium1.37e-0769
hemolymphoid system3.43e-0748
immune system3.43e-0748
respiratory system8.17e-0742


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)
MA0003.12.63694
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.11.54572
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.11.40661
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
MA0055.10.282934
MA0056.10
MA0057.12.16719
MA0058.10.341628
MA0059.10.353484
MA0060.10.574356
MA0061.11.86175
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.657844
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.00296875
MA0074.10.531046
MA0076.12.32425
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.853781
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.823589
MA0106.11.51778
MA0107.10.814533
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.11.36991
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.11.63575
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.12.32782
MA0139.10.977634
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.11.35361
MA0146.11.72764
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.25.92123
MA0035.20.524137
MA0039.21.36565
MA0138.20.675599
MA0002.20.172399
MA0137.20.863775
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.0804339
MA0156.12.32016
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.11.4435
MA0163.12.26891
MA0164.10.551114
MA0080.21.48111
MA0018.20.560731
MA0099.20.669311
MA0079.24.20879
MA0102.21.59466
MA0258.10.210437
MA0259.10.643936
MA0442.10
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