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MCL coexpression mm9:1791: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0016080;synaptic vesicle targeting;0.0240970418475486;192167!GO:0006903;vesicle targeting;0.0240970418475486;192167!GO:0042043;neurexin binding;0.0240970418475486;192167!GO:0016079;synaptic vesicle exocytosis;0.0240970418475486;192167!GO:0051650;establishment of vesicle localization;0.0240970418475486;192167!GO:0051648;vesicle localization;0.0240970418475486;192167!GO:0005003;ephrin receptor activity;0.0240970418475486;13839!GO:0007416;synaptogenesis;0.0270995143755786;192167!GO:0051656;establishment of organelle localization;0.0270995143755786;192167!GO:0048489;synaptic vesicle transport;0.0270995143755786;192167!GO:0051640;organelle localization;0.0270995143755786;192167!GO:0045664;regulation of neuron differentiation;0.0270995143755786;192167!GO:0050808;synapse organization and biogenesis;0.0407460835267628;192167!GO:0007269;neurotransmitter secretion;0.0438465372469897;192167!GO:0004714;transmembrane receptor protein tyrosine kinase activity;0.0481280481196195;13839!GO:0045055;regulated secretory pathway;0.0481280481196195;192167!
|ontology_enrichment_celltype=CL:0000117!1.03e-16!23;CL:0000337!1.03e-16!23;CL:0000540!4.04e-16!33;CL:0000047!4.04e-16!33;CL:0000031!4.04e-16!33;CL:0000404!4.04e-16!33;CL:0000221!3.21e-14!44;CL:0000133!3.21e-14!44;CL:0002319!4.83e-14!43;CL:0000393!1.27e-11!39;CL:0000211!1.27e-11!39;CL:0000055!1.38e-10!49
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!1.20e-34!64;UBERON:0003075!1.20e-34!64;UBERON:0007284!1.20e-34!64;UBERON:0004121!5.12e-34!95;UBERON:0000924!5.12e-34!95;UBERON:0006601!5.12e-34!95;UBERON:0001016!6.23e-33!75;UBERON:0001017!4.35e-32!73;UBERON:0003056!1.09e-30!49;UBERON:0000073!1.51e-30!54;UBERON:0010371!8.58e-30!73;UBERON:0001049!1.93e-28!52;UBERON:0005068!1.93e-28!52;UBERON:0006241!1.93e-28!52;UBERON:0007135!1.93e-28!52;UBERON:0000955!1.78e-25!47;UBERON:0006238!1.78e-25!47;UBERON:0002616!1.51e-24!46;UBERON:0003080!3.30e-24!40;UBERON:0002780!1.33e-23!39;UBERON:0001890!1.33e-23!39;UBERON:0006240!1.33e-23!39;UBERON:0002020!1.64e-23!34;UBERON:0010314!1.51e-21!92;UBERON:0003528!2.40e-20!29;UBERON:0002791!2.40e-20!29;UBERON:0001893!2.40e-20!29;UBERON:0000956!1.82e-15!21;UBERON:0001869!1.82e-15!21;UBERON:0000203!1.82e-15!21;UBERON:0002619!2.34e-12!17;UBERON:0002021!1.79e-08!10;UBERON:0000411!1.79e-08!10;UBERON:0001950!1.79e-08!10;UBERON:0000020!3.30e-07!12;UBERON:0001032!3.30e-07!12;UBERON:0004456!3.30e-07!12;UBERON:0000970!4.48e-07!9;UBERON:0000019!4.48e-07!9;UBERON:0000047!4.48e-07!9;UBERON:0010312!4.48e-07!9;UBERON:0004088!4.48e-07!9;UBERON:0002104!4.48e-07!9;UBERON:0001456!4.48e-07!9;UBERON:0003072!4.48e-07!9;UBERON:0004128!4.48e-07!9;UBERON:0003071!4.48e-07!9
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.02681,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.370407,3.93412,0.702872,0.812978,0.728641,0.424775,0,0.930881,0.397593,0.283802,1.0421,0.489529,0.145201,0.727684,0.404661,0.537749,0.757752,0.754069,0.641282,0.456327,1.87618,0.626183,1.03545,1.02297,0.704734,0.425309,0.20704,2.66119,1.66799,0.360612,0.328675,1.03785,0.631725,0.134724,0.426986,0.84962,2.45957,0.847828,1.58288,0.746467,0.459555,0.912738,0.786094,1.17664,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,2.08407,1.76944,0.943088,1.33705,1.68977,1.00999,1.54147,1.26875,0.30684,20.9395,1.23259,0.257421,0.245132,0.253065,0.835925,0.997094,1.23692,0.308173,0.948899,0.794502,0.293164,1.1148,0.272382,0.618102,1.20595,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,24.908,0.3366,1.46478,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,0.653843,21.8367,3.1533,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,5.18669,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,2.2879,0.724289,1.04166,1.33551,0.416189,1.14546,1.45154,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,15.295,1.18223,1.62749,0.749664,1.26545,0.787153,0.438007,0.555203,1.39093,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.0513167
|tfbs_overrepresentation_jaspar=MA0003.1;1.36559,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.736185,MA0017.1;1.14026,MA0019.1;2.02888,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;0.43138,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;1.12075,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.602741,MA0056.1;0,MA0057.1;1.68574,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.330907,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;0.197245,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;0.0176764,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;0.148348,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;0.567278,MA0093.1;0.440484,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;0.248108,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;0.949408,MA0115.1;1.16466,MA0116.1;0.419688,MA0117.1;1.13165,MA0119.1;0.524046,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;3.09117,MA0140.1;1.6611,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;2.12682,MA0146.1;0.822925,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;0.489701,MA0138.2;0.861035,MA0002.2;1.47075,MA0137.2;0.479301,MA0104.2;1.52809,MA0047.2;0.75686,MA0112.2;0.157681,MA0065.2;0.158101,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;1.11105,MA0155.1;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;1.35147,MA0163.1;0.0644585,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;1.7149,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}

Latest revision as of 17:30, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr3:26230826..26230839,-p6@Nlgn1
Mm9::chr5:84846323..84846334,-p3@Epha5
Mm9::chr5:84846349..84846362,-p2@Epha5
Mm9::chr5:84846393..84846414,-p1@Epha5
Mm9::chr5:84846420..84846425,-p4@Epha5


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:0016080synaptic vesicle targeting0.0240970418475486
GO:0006903vesicle targeting0.0240970418475486
GO:0042043neurexin binding0.0240970418475486
GO:0016079synaptic vesicle exocytosis0.0240970418475486
GO:0051650establishment of vesicle localization0.0240970418475486
GO:0051648vesicle localization0.0240970418475486
GO:0005003ephrin receptor activity0.0240970418475486
GO:0007416synaptogenesis0.0270995143755786
GO:0051656establishment of organelle localization0.0270995143755786
GO:0048489synaptic vesicle transport0.0270995143755786
GO:0051640organelle localization0.0270995143755786
GO:0045664regulation of neuron differentiation0.0270995143755786
GO:0050808synapse organization and biogenesis0.0407460835267628
GO:0007269neurotransmitter secretion0.0438465372469897
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0481280481196195
GO:0045055regulated secretory pathway0.0481280481196195



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
neurectoderm1.20e-3464
neural plate1.20e-3464
presumptive neural plate1.20e-3464
ectoderm-derived structure5.12e-3495
ectoderm5.12e-3495
presumptive ectoderm5.12e-3495
nervous system6.23e-3375
central nervous system4.35e-3273
pre-chordal neural plate1.09e-3049
regional part of nervous system1.51e-3054
ecto-epithelium8.58e-3073
neural tube1.93e-2852
neural rod1.93e-2852
future spinal cord1.93e-2852
neural keel1.93e-2852
brain1.78e-2547
future brain1.78e-2547
regional part of brain1.51e-2446
anterior neural tube3.30e-2440
regional part of forebrain1.33e-2339
forebrain1.33e-2339
future forebrain1.33e-2339
gray matter1.64e-2334
structure with developmental contribution from neural crest1.51e-2192
brain grey matter2.40e-2029
regional part of telencephalon2.40e-2029
telencephalon2.40e-2029
cerebral cortex1.82e-1521
cerebral hemisphere1.82e-1521
pallium1.82e-1521
regional part of cerebral cortex2.34e-1217
occipital lobe1.79e-0810
visual cortex1.79e-0810
neocortex1.79e-0810
sense organ3.30e-0712
sensory system3.30e-0712
entire sense organ system3.30e-0712
eye4.48e-079
camera-type eye4.48e-079
simple eye4.48e-079
immature eye4.48e-079
ocular region4.48e-079
visual system4.48e-079
face4.48e-079
optic cup4.48e-079
optic vesicle4.48e-079
eye primordium4.48e-079


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)
MA0003.11.36559
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.736185
MA0017.11.14026
MA0019.12.02888
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
MA0048.11.12075
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.602741
MA0056.10
MA0057.11.68574
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
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
MA0073.10.0176764
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
MA0113.10.780358
MA0114.10.949408
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
MA0139.13.09117
MA0140.11.6611
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.12.12682
MA0146.10.822925
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.489701
MA0138.20.861035
MA0002.21.47075
MA0137.20.479301
MA0104.21.52809
MA0047.20.75686
MA0112.20.157681
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.11.11105
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.11.35147
MA0163.10.0644585
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.21.7149
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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