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MCL coexpression mm9:888: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000055!3.74e-15!49;CL:0002319!2.94e-13!43;CL:0000117!5.31e-13!23;CL:0000337!5.31e-13!23;CL:0000221!8.24e-13!44;CL:0000133!8.24e-13!44;CL:0000393!1.57e-12!39;CL:0000211!1.57e-12!39;CL:0000540!1.00e-10!33;CL:0000047!1.00e-10!33;CL:0000031!1.00e-10!33;CL:0000404!1.00e-10!33;CL:0002321!1.38e-08!70;CL:0000723!1.89e-07!91;CL:0000048!1.89e-07!91;CL:0000548!6.76e-07!115;CL:0000255!6.76e-07!115;CL:0000034!7.60e-07!97
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.04e-25!73;UBERON:0001016!1.86e-25!75;UBERON:0000073!3.17e-23!54;UBERON:0001049!9.99e-22!52;UBERON:0005068!9.99e-22!52;UBERON:0006241!9.99e-22!52;UBERON:0007135!9.99e-22!52;UBERON:0004121!3.10e-19!95;UBERON:0000924!3.10e-19!95;UBERON:0006601!3.10e-19!95;UBERON:0002020!3.11e-19!34;UBERON:0002346!5.15e-19!64;UBERON:0003075!5.15e-19!64;UBERON:0007284!5.15e-19!64;UBERON:0000955!1.03e-18!47;UBERON:0006238!1.03e-18!47;UBERON:0002616!4.16e-18!46;UBERON:0003528!3.43e-16!29;UBERON:0002791!3.43e-16!29;UBERON:0001893!3.43e-16!29;UBERON:0003080!3.10e-15!40;UBERON:0010371!6.53e-15!73;UBERON:0002780!9.12e-15!39;UBERON:0001890!9.12e-15!39;UBERON:0006240!9.12e-15!39;UBERON:0003056!1.78e-12!49;UBERON:0000956!3.59e-12!21;UBERON:0001869!3.59e-12!21;UBERON:0000203!3.59e-12!21;UBERON:0010314!4.91e-11!92;UBERON:0000025!1.47e-10!114;UBERON:0002619!1.74e-10!17;UBERON:0004111!3.31e-10!122;UBERON:0002021!5.90e-08!10;UBERON:0000411!5.90e-08!10;UBERON:0001950!5.90e-08!10;UBERON:0003076!2.80e-07!12;UBERON:0003057!2.80e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.393008,1.2286,0.367606,0.434198,0.720982,0.448401,0.538088,0.515265,0.535519,0.170907,0.494602,0.526159,0.173454,0.550255,2.12798,0,0.742571,0.252772,0.483643,0.620214,0.332107,0.837949,1.35437,0.258745,0.374936,0.577606,0.909128,0.469052,0.303071,0.376624,1.15331,0.843667,0.250677,0.425071,0.757987,0.60397,0.242032,0.522578,0.221921,1.08217,0.712303,0.460258,0.204736,0.27776,0.209497,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.844204,0.513517,1.41162,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.0665967,1.03623,0.433216,0.409836,0.839631,0.651651,0.806481,0.336166,1.01677,0.759925,0.612313,0.167672,0.920903,0.491838,0.0299392,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.982739,0.859272,0.663249,0.332938,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.887702,1.00333,0.96962,0.337254,0.499714,1.21576,0.254749,0.0359654,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,1.16523,0.666107,1.9792,0.403515,0.261837,0.120154,0.203102,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.0628627
}}

Latest revision as of 16:03, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:115941080..115941099,-p@chr11:115941080..115941099
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Mm9::chr11:115941930..115941942,-p@chr11:115941930..115941942
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Mm9::chr11:115941977..115941989,-p@chr11:115941977..115941989
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Mm9::chr11:76235757..76235770,-p@chr11:76235757..76235770
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Mm9::chr15:79940875..79940915,+p@chr15:79940875..79940915
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Mm9::chr6:124952100..124952114,+p@chr6:124952100..124952114
+
Mm9::chr8:74135129..74135148,+p@chr8:74135129..74135148
+
Mm9::chr8:74135149..74135159,+p@chr8:74135149..74135159
+


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:0009103lipopolysaccharide biosynthetic process0.0187315136405807
GO:0008653lipopolysaccharide metabolic process0.0187315136405807
GO:0033692cellular polysaccharide biosynthetic process0.0296371085376566
GO:0000271polysaccharide biosynthetic process0.0296371085376566
GO:0005976polysaccharide metabolic process0.0488002655473285
GO:0044264cellular polysaccharide metabolic process0.0488002655473285



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
central nervous system1.04e-2573
nervous system1.86e-2575
regional part of nervous system3.17e-2354
neural tube9.99e-2252
neural rod9.99e-2252
future spinal cord9.99e-2252
neural keel9.99e-2252
ectoderm-derived structure3.10e-1995
ectoderm3.10e-1995
presumptive ectoderm3.10e-1995
gray matter3.11e-1934
neurectoderm5.15e-1964
neural plate5.15e-1964
presumptive neural plate5.15e-1964
brain1.03e-1847
future brain1.03e-1847
regional part of brain4.16e-1846
brain grey matter3.43e-1629
regional part of telencephalon3.43e-1629
telencephalon3.43e-1629
anterior neural tube3.10e-1540
ecto-epithelium6.53e-1573
regional part of forebrain9.12e-1539
forebrain9.12e-1539
future forebrain9.12e-1539
pre-chordal neural plate1.78e-1249
cerebral cortex3.59e-1221
cerebral hemisphere3.59e-1221
pallium3.59e-1221
structure with developmental contribution from neural crest4.91e-1192
tube1.47e-10114
regional part of cerebral cortex1.74e-1017
anatomical conduit3.31e-10122
occipital lobe5.90e-0810
visual cortex5.90e-0810
neocortex5.90e-0810
posterior neural tube2.80e-0712
chordal neural plate2.80e-0712


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)
MA0003.10.241599
MA0004.10.434673
MA0006.11.37063
MA0007.10.419994
MA0009.12.02076
MA0014.10.012738
MA0017.10.804572
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
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
MA0048.10.335404
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.11.2091
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.931383
MA0060.10.197678
MA0061.11.19505
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.0449725
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.11.29043
MA0089.10
MA0090.11.03628
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.950493
MA0103.10.827743
MA0105.10.41549
MA0106.10.626997
MA0107.10.814533
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.633896
MA0115.12.22418
MA0116.12.93249
MA0117.10.937363
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
MA0139.10.169849
MA0140.10.519484
MA0141.10.869985
MA0142.10.761136
MA0143.10.615203
MA0144.10.640537
MA0145.10.0701568
MA0146.10.636109
MA0147.11.24068
MA0148.10.450593
MA0149.10.367458
MA0062.20.426733
MA0035.20.524137
MA0039.20.254826
MA0138.20.675599
MA0002.20.513194
MA0137.20.32312
MA0104.21.64215
MA0047.20.576767
MA0112.20.2464
MA0065.22.46367
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.12.25112
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.13.62871
MA0160.11.14982
MA0161.10
MA0162.10.0211019
MA0163.10.0836563
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.174131
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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