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MCL coexpression mm9:1715: Difference between revisions

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{{MCL_coexpression_mm9
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fraction;6.13115797569772e-06;93699,93716,93724,93723!GO:0000267;cell fraction;6.13115797569772e-06;93699,93716,93724,93723!GO:0022610;biological adhesion;6.13115797569772e-06;93699,93716,93724,93723!GO:0007155;cell adhesion;6.13115797569772e-06;93699,93716,93724,93723!GO:0005509;calcium ion binding;1.52263658322643e-05;93699,93716,93724,93723!GO:0043169;cation binding;0.00342495576586387;93699,93716,93724,93723!GO:0046872;metal ion binding;0.00387237709599195;93699,93716,93724,93723!GO:0043167;ion binding;0.00387237709599195;93699,93716,93724,93723!GO:0016339;calcium-dependent cell-cell adhesion;0.00559615603801538;93724!GO:0030427;site of polarized growth;0.00686518770334967;93699!GO:0030426;growth cone;0.00686518770334967;93699!GO:0005515;protein binding;0.00878908899684793;93699,93716,93724,93723!GO:0016021;integral to membrane;0.0152531132314203;93699,93716,93724,93723!GO:0031224;intrinsic to membrane;0.0152531132314203;93699,93716,93724,93723!GO:0044425;membrane part;0.0196580359574477;93699,93716,93724,93723!GO:0016020;membrane;0.0366972763483849;93699,93716,93724,93723!GO:0005911;intercellular 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|gostat_on_MCL_coexpression=GO:0005624;membrane fraction;6.13115797569772e-06;93699,93716,93724,93723!GO:0000267;cell fraction;6.13115797569772e-06;93699,93716,93724,93723!GO:0022610;biological adhesion;6.13115797569772e-06;93699,93716,93724,93723!GO:0007155;cell adhesion;6.13115797569772e-06;93699,93716,93724,93723!GO:0005509;calcium ion binding;1.52263658322643e-05;93699,93716,93724,93723!GO:0043169;cation binding;0.00342495576586387;93699,93716,93724,93723!GO:0046872;metal ion binding;0.00387237709599195;93699,93716,93724,93723!GO:0043167;ion binding;0.00387237709599195;93699,93716,93724,93723!GO:0016339;calcium-dependent cell-cell adhesion;0.00559615603801538;93724!GO:0030427;site of polarized growth;0.00686518770334967;93699!GO:0030426;growth cone;0.00686518770334967;93699!GO:0005515;protein binding;0.00878908899684793;93699,93716,93724,93723!GO:0016021;integral to membrane;0.0152531132314203;93699,93716,93724,93723!GO:0031224;intrinsic to membrane;0.0152531132314203;93699,93716,93724,93723!GO:0044425;membrane part;0.0196580359574477;93699,93716,93724,93723!GO:0016020;membrane;0.0366972763483849;93699,93716,93724,93723!GO:0005911;intercellular junction;0.0439313037485811;93724!
|ontology_enrichment_celltype=CL:0000117!2.99e-10!23;CL:0000337!2.99e-10!23;CL:0000221!9.74e-09!44;CL:0000133!9.74e-09!44;CL:0002319!1.47e-08!43;CL:0000540!9.23e-07!33;CL:0000047!9.23e-07!33;CL:0000031!9.23e-07!33;CL:0000404!9.23e-07!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!4.91e-28!64;UBERON:0003075!4.91e-28!64;UBERON:0007284!4.91e-28!64;UBERON:0004121!6.36e-28!95;UBERON:0000924!6.36e-28!95;UBERON:0006601!6.36e-28!95;UBERON:0000073!3.80e-27!54;UBERON:0001016!1.32e-26!75;UBERON:0001049!1.53e-26!52;UBERON:0005068!1.53e-26!52;UBERON:0006241!1.53e-26!52;UBERON:0007135!1.53e-26!52;UBERON:0010371!1.77e-26!73;UBERON:0010314!2.15e-26!92;UBERON:0001017!3.98e-26!73;UBERON:0000955!4.44e-24!47;UBERON:0006238!4.44e-24!47;UBERON:0003056!5.24e-24!49;UBERON:0002616!2.50e-23!46;UBERON:0003080!1.00e-20!40;UBERON:0002780!3.92e-20!39;UBERON:0001890!3.92e-20!39;UBERON:0006240!3.92e-20!39;UBERON:0002020!4.12e-18!34;UBERON:0003528!9.74e-16!29;UBERON:0002791!9.74e-16!29;UBERON:0001893!9.74e-16!29;UBERON:0000025!4.53e-14!114;UBERON:0004111!1.12e-13!122;UBERON:0000956!1.71e-12!21;UBERON:0001869!1.71e-12!21;UBERON:0000203!1.71e-12!21;UBERON:0000468!7.89e-11!333;UBERON:0002619!1.97e-10!17;UBERON:0000922!9.63e-09!320;UBERON:0002021!9.70e-08!10;UBERON:0000411!9.70e-08!10;UBERON:0001950!9.70e-08!10;UBERON:0000479!7.47e-07!349
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.145201,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.253145,0.425309,0.0566307,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.0637209,1.44282,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.257421,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.796301,1.1148,0.0793594,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,1.06179,0.356133,0.3366,0.806207,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.0998646,0.607321,2.14787,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,1.06895,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.133815,1.18223,0.343194,1.77291,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.0513167
}}

Latest revision as of 17:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr18:37833957..37834019,+p2@Pcdhga11
p2@Pcdhga12
p2@Pcdhga3
p2@Pcdhga8
p2@Pcdhga9
p2@Pcdhgb6
p2@Pcdhgc3
p2@Pcdhgc4
p2@Pcdhgc5
Mm9::chr18:37839908..37839961,+p1@Pcdhgb1
Mm9::chr18:37885375..37885408,+p8@Pcdhga11
p8@Pcdhga12
p8@Pcdhga3
p8@Pcdhga8
p8@Pcdhga9
p8@Pcdhgb6
p8@Pcdhgc3
p8@Pcdhgc4
p8@Pcdhgc5
Mm9::chr18:37915372..37915421,+p4@Pcdhga11
p4@Pcdhga12
p4@Pcdhga3
p4@Pcdhga8
p4@Pcdhga9
p4@Pcdhgb6
p4@Pcdhgc3
p4@Pcdhgc4
p4@Pcdhgc5
Mm9::chr18:37925612..37925662,+p9@Pcdhga11
p9@Pcdhga12
p9@Pcdhga3
p9@Pcdhga8
p9@Pcdhga9
p9@Pcdhgb6
p9@Pcdhgc3
p9@Pcdhgc4
p9@Pcdhgc5


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:0005624membrane fraction6.13115797569772e-06
GO:0000267cell fraction6.13115797569772e-06
GO:0022610biological adhesion6.13115797569772e-06
GO:0007155cell adhesion6.13115797569772e-06
GO:0005509calcium ion binding1.52263658322643e-05
GO:0043169cation binding0.00342495576586387
GO:0046872metal ion binding0.00387237709599195
GO:0043167ion binding0.00387237709599195
GO:0016339calcium-dependent cell-cell adhesion0.00559615603801538
GO:0030427site of polarized growth0.00686518770334967
GO:0030426growth cone0.00686518770334967
GO:0005515protein binding0.00878908899684793
GO:0016021integral to membrane0.0152531132314203
GO:0031224intrinsic to membrane0.0152531132314203
GO:0044425membrane part0.0196580359574477
GO:0016020membrane0.0366972763483849
GO:0005911intercellular junction0.0439313037485811



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
CNS neuron (sensu Vertebrata)2.99e-1023
neuroblast (sensu Vertebrata)2.99e-1023
ectodermal cell9.74e-0944
neurectodermal cell9.74e-0944
neural cell1.47e-0843
neuron9.23e-0733
neuronal stem cell9.23e-0733
neuroblast9.23e-0733
electrically signaling cell9.23e-0733

Uber Anatomy
Ontology termp-valuen
neurectoderm4.91e-2864
neural plate4.91e-2864
presumptive neural plate4.91e-2864
ectoderm-derived structure6.36e-2895
ectoderm6.36e-2895
presumptive ectoderm6.36e-2895
regional part of nervous system3.80e-2754
nervous system1.32e-2675
neural tube1.53e-2652
neural rod1.53e-2652
future spinal cord1.53e-2652
neural keel1.53e-2652
ecto-epithelium1.77e-2673
structure with developmental contribution from neural crest2.15e-2692
central nervous system3.98e-2673
brain4.44e-2447
future brain4.44e-2447
pre-chordal neural plate5.24e-2449
regional part of brain2.50e-2346
anterior neural tube1.00e-2040
regional part of forebrain3.92e-2039
forebrain3.92e-2039
future forebrain3.92e-2039
gray matter4.12e-1834
brain grey matter9.74e-1629
regional part of telencephalon9.74e-1629
telencephalon9.74e-1629
tube4.53e-14114
anatomical conduit1.12e-13122
cerebral cortex1.71e-1221
cerebral hemisphere1.71e-1221
pallium1.71e-1221
multi-cellular organism7.89e-11333
regional part of cerebral cortex1.97e-1017
embryo9.63e-09320
occipital lobe9.70e-0810
visual cortex9.70e-0810
neocortex9.70e-0810
tissue7.47e-07349


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)
MA0003.10.0185483
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.0502051
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.10.881183
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.103695
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.13.06168
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.8026
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.0604336
MA0147.10.378658
MA0148.11.50563
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.0102623
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.11.78802
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.0699535
MA0163.10.0644585
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.0381166
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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