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MCL coexpression mm9:459: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0000073!5.95e-26!54;UBERON:0001049!9.53e-26!52;UBERON:0005068!9.53e-26!52;UBERON:0006241!9.53e-26!52;UBERON:0007135!9.53e-26!52;UBERON:0002346!1.72e-24!64;UBERON:0003075!1.72e-24!64;UBERON:0007284!1.72e-24!64;UBERON:0002020!3.25e-24!34;UBERON:0000955!8.76e-22!47;UBERON:0006238!8.76e-22!47;UBERON:0010371!1.60e-21!73;UBERON:0003056!3.07e-21!49;UBERON:0002616!4.73e-21!46;UBERON:0001017!8.03e-21!73;UBERON:0003080!1.79e-20!40;UBERON:0003528!6.76e-20!29;UBERON:0002791!6.76e-20!29;UBERON:0001893!6.76e-20!29;UBERON:0002780!8.81e-20!39;UBERON:0001890!8.81e-20!39;UBERON:0006240!8.81e-20!39;UBERON:0001016!1.03e-19!75;UBERON:0004121!9.25e-18!95;UBERON:0000924!9.25e-18!95;UBERON:0006601!9.25e-18!95;UBERON:0010314!4.66e-14!92;UBERON:0000956!1.12e-13!21;UBERON:0001869!1.12e-13!21;UBERON:0000203!1.12e-13!21;UBERON:0002619!3.03e-10!17;UBERON:0002021!6.39e-08!10;UBERON:0000411!6.39e-08!10;UBERON:0001950!6.39e-08!10;UBERON:0002420!1.87e-07!8;UBERON:0007245!1.87e-07!8;UBERON:0010009!1.87e-07!8;UBERON:0010011!1.87e-07!8;UBERON:0000454!1.87e-07!8
|tfbs_overrepresentation_for_novel_motifs=0.556227,0.732102,0.984016,0.221468,0.325044,0.232532,0.305009,0.186307,0.768345,0.491359,0.742008,0.295134,0.416678,0.315149,0.108498,0,0.482714,0.645746,1.04704,0.599319,0.146132,0.242916,0.844218,0.663197,0.523846,0.338177,0.156743,0.248835,1.29108,0.78695,1.24431,0.574932,0.639629,0.314034,1.72344,3.20462,0.294993,0.292182,0.262298,2.92404,0.318773,1.25947,0.86683,0.354562,0.713083,0.610939,0.41191,0.26128,0.725187,0.128181,0.467043,0.947989,0.100464,0.7073,0.723811,0.85924,0.133938,0.284741,0.611426,0.319396,0.556492,0.369066,0.215066,0.456979,0.330403,0.493315,0.854035,1.19441,0.552202,1.05011,1.48716,0.0523282,0.261967,0.755651,0.322986,0.297446,0.133371,0.401969,0.540754,0.148967,0.195767,0.498379,0.36783,0.177942,0.646739,2.2113,0.103037,0.0254035,0.416206,1.35441,0.92132,0.6514,0.586758,0.102076,0.545298,0.49924,0.722691,0.589355,0.412133,0.681961,0.295113,0.574674,0.690844,0.467576,0.466632,0.677777,0.52055,0.25809,0.463457,0.451142,0.185018,0.692526,0.457145,0.273484,0.928143,0.315992,2.22139,1.85868,0.483885,0.289365,0.760792,0.438354,0.339713,0.40118,0.980682,0.544138,0.311744,0.580495,0.852575,0.339019,0.67485,0.215942,0.824167,0.332514,0.949083,0.11332,0.196278,0.24296,0.901468,1.71991,1.32292,0.85857,0.349901,0.584599,0.46084,0.679396,0.414644,1.68046,0.575158,0.672242,0.498918,0.377356,0.708784,0.881649,0.331737,0.786435,0.361851,0.115836,0.188342,0.196072,0.910663,0.645939,0.544546,0.539942,0.457889,0.325532,0.293289,0.293837,0.999778
|tfbs_overrepresentation_jaspar=MA0003.1;2.07644,MA0004.1;0.631712,MA0006.1;0.344361,MA0007.1;0.604993,MA0009.1;0.599391,MA0014.1;1.24107,MA0017.1;0.122138,MA0019.1;0.434009,MA0024.1;0.558971,MA0025.1;0.819843,MA0027.1;2.21717,MA0028.1;0.360944,MA0029.1;0.53905,MA0030.1;0.545058,MA0031.1;0.512616,MA0038.1;0.33811,MA0040.1;0.611015,MA0041.1;2.19489,MA0042.1;0.926457,MA0043.1;0.689898,MA0046.1;0.632833,MA0048.1;1.39913,MA0050.1;0.251816,MA0051.1;0.345658,MA0052.1;0.618515,MA0055.1;0.0964477,MA0056.1;0,MA0057.1;0.939001,MA0058.1;0.90709,MA0059.1;0.942177,MA0060.1;0.0623353,MA0061.1;0.267107,MA0063.1;0,MA0066.1;0.328887,MA0067.1;0.92691,MA0068.1;2.22212,MA0069.1;0.618831,MA0070.1;0.609808,MA0071.1;0.251158,MA0072.1;0.601934,MA0073.1;3.7883,MA0074.1;0.299171,MA0076.1;0.134359,MA0077.1;0.581866,MA0078.1;0.37382,MA0081.1;0.525479,MA0083.1;0.68915,MA0084.1;1.24749,MA0087.1;0.648637,MA0088.1;0.969,MA0089.1;0,MA0090.1;0.196267,MA0091.1;0.231874,MA0092.1;0.196497,MA0093.1;1.23271,MA0095.1;0,MA0098.1;0,MA0100.1;0.289731,MA0101.1;0.167439,MA0103.1;0.404646,MA0105.1;0.303578,MA0106.1;0.990986,MA0107.1;0.394565,MA0108.2;0.454274,MA0109.1;0,MA0111.1;0.206727,MA0113.1;0.356344,MA0114.1;0.0762439,MA0115.1;0.692537,MA0116.1;1.69621,MA0117.1;0.662171,MA0119.1;0.16785,MA0122.1;0.680832,MA0124.1;0.875485,MA0125.1;0.804312,MA0130.1;0,MA0131.1;1.92675,MA0132.1;0,MA0133.1;0,MA0135.1;0.724328,MA0136.1;0.315568,MA0139.1;0.181201,MA0140.1;0.289637,MA0141.1;0.141822,MA0142.1;0.499475,MA0143.1;1.72227,MA0144.1;0.566612,MA0145.1;0.135509,MA0146.1;1.16378,MA0147.1;0.599447,MA0148.1;0.23425,MA0149.1;0.510517,MA0062.2;0.0332891,MA0035.2;0.293466,MA0039.2;1.42027,MA0138.2;0.423003,MA0002.2;0.413675,MA0137.2;0.432446,MA0104.2;0.449737,MA0047.2;0.337465,MA0112.2;0.73225,MA0065.2;1.0422,MA0150.1;0.210447,MA0151.1;0,MA0152.1;0.337555,MA0153.1;0.740107,MA0154.1;0.215016,MA0155.1;0.32315,MA0156.1;0.133796,MA0157.1;0.47062,MA0158.1;0,MA0159.1;1.04823,MA0160.1;0.23657,MA0161.1;0,MA0162.1;2.38061,MA0163.1;2.23838,MA0164.1;0.315868,MA0080.2;0.125629,MA0018.2;0.323932,MA0099.2;0.417463,MA0079.2;14.2965,MA0102.2;1.29919,MA0258.1;0.0692929,MA0259.1;0.965484,MA0442.1;0
}}

Latest revision as of 15:20, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:23976906..23976924,+p@chr11:23976906..23976924
+
Mm9::chr11:23978229..23978268,+p8@Bcl11a
Mm9::chr11:23978270..23978290,+p9@Bcl11a
Mm9::chr11:23978291..23978323,+p7@Bcl11a
Mm9::chr12:112615997..112616010,-p6@Cdc42bpb
Mm9::chr14:121434378..121434408,+p6@Farp1
Mm9::chr15:82794178..82794195,-p@chr15:82794178..82794195
-
Mm9::chr15:98765033..98765043,-p4@Gm5620
p4@Tuba1b
Mm9::chr16:72663276..72663289,+p6@Robo1
Mm9::chr17:8994505..8994547,+p2@Pde10a
Mm9::chr17:8994571..8994586,+p11@Pde10a
Mm9::chr18:67247886..67247902,+p6@Gnal
Mm9::chr5:35260167..35260194,+p@chr5:35260167..35260194
+
Mm9::chr5:36873259..36873278,-p5@Tbc1d14
Mm9::chr5:92566795..92566812,-p@chr5:92566795..92566812
-
Mm9::chr9:42879451..42879465,-p@chr9:42879451..42879465
-


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

no results for this coexpression

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
regional part of nervous system5.95e-2654
neural tube9.53e-2652
neural rod9.53e-2652
future spinal cord9.53e-2652
neural keel9.53e-2652
neurectoderm1.72e-2464
neural plate1.72e-2464
presumptive neural plate1.72e-2464
gray matter3.25e-2434
brain8.76e-2247
future brain8.76e-2247
ecto-epithelium1.60e-2173
pre-chordal neural plate3.07e-2149
regional part of brain4.73e-2146
central nervous system8.03e-2173
anterior neural tube1.79e-2040
brain grey matter6.76e-2029
regional part of telencephalon6.76e-2029
telencephalon6.76e-2029
regional part of forebrain8.81e-2039
forebrain8.81e-2039
future forebrain8.81e-2039
nervous system1.03e-1975
ectoderm-derived structure9.25e-1895
ectoderm9.25e-1895
presumptive ectoderm9.25e-1895
structure with developmental contribution from neural crest4.66e-1492
cerebral cortex1.12e-1321
cerebral hemisphere1.12e-1321
pallium1.12e-1321
regional part of cerebral cortex3.03e-1017
occipital lobe6.39e-0810
visual cortex6.39e-0810
neocortex6.39e-0810
basal ganglion1.87e-078
nuclear complex of neuraxis1.87e-078
aggregate regional part of brain1.87e-078
collection of basal ganglia1.87e-078
cerebral subcortex1.87e-078


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)
MA0003.12.07644
MA0004.10.631712
MA0006.10.344361
MA0007.10.604993
MA0009.10.599391
MA0014.11.24107
MA0017.10.122138
MA0019.10.434009
MA0024.10.558971
MA0025.10.819843
MA0027.12.21717
MA0028.10.360944
MA0029.10.53905
MA0030.10.545058
MA0031.10.512616
MA0038.10.33811
MA0040.10.611015
MA0041.12.19489
MA0042.10.926457
MA0043.10.689898
MA0046.10.632833
MA0048.11.39913
MA0050.10.251816
MA0051.10.345658
MA0052.10.618515
MA0055.10.0964477
MA0056.10
MA0057.10.939001
MA0058.10.90709
MA0059.10.942177
MA0060.10.0623353
MA0061.10.267107
MA0063.10
MA0066.10.328887
MA0067.10.92691
MA0068.12.22212
MA0069.10.618831
MA0070.10.609808
MA0071.10.251158
MA0072.10.601934
MA0073.13.7883
MA0074.10.299171
MA0076.10.134359
MA0077.10.581866
MA0078.10.37382
MA0081.10.525479
MA0083.10.68915
MA0084.11.24749
MA0087.10.648637
MA0088.10.969
MA0089.10
MA0090.10.196267
MA0091.10.231874
MA0092.10.196497
MA0093.11.23271
MA0095.10
MA0098.10
MA0100.10.289731
MA0101.10.167439
MA0103.10.404646
MA0105.10.303578
MA0106.10.990986
MA0107.10.394565
MA0108.20.454274
MA0109.10
MA0111.10.206727
MA0113.10.356344
MA0114.10.0762439
MA0115.10.692537
MA0116.11.69621
MA0117.10.662171
MA0119.10.16785
MA0122.10.680832
MA0124.10.875485
MA0125.10.804312
MA0130.10
MA0131.11.92675
MA0132.10
MA0133.10
MA0135.10.724328
MA0136.10.315568
MA0139.10.181201
MA0140.10.289637
MA0141.10.141822
MA0142.10.499475
MA0143.11.72227
MA0144.10.566612
MA0145.10.135509
MA0146.11.16378
MA0147.10.599447
MA0148.10.23425
MA0149.10.510517
MA0062.20.0332891
MA0035.20.293466
MA0039.21.42027
MA0138.20.423003
MA0002.20.413675
MA0137.20.432446
MA0104.20.449737
MA0047.20.337465
MA0112.20.73225
MA0065.21.0422
MA0150.10.210447
MA0151.10
MA0152.10.337555
MA0153.10.740107
MA0154.10.215016
MA0155.10.32315
MA0156.10.133796
MA0157.10.47062
MA0158.10
MA0159.11.04823
MA0160.10.23657
MA0161.10
MA0162.12.38061
MA0163.12.23838
MA0164.10.315868
MA0080.20.125629
MA0018.20.323932
MA0099.20.417463
MA0079.214.2965
MA0102.21.29919
MA0258.10.0692929
MA0259.10.965484
MA0442.10
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