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MCL coexpression mm9:2859: Difference between revisions

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{{MCL_coexpression_mm9
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coat of coated pit;0.0146463956248649;74325!GO:0030130;clathrin coat of trans-Golgi network vesicle;0.0146463956248649;74325!GO:0012510;trans-Golgi network transport vesicle membrane;0.0146463956248649;74325!GO:0030660;Golgi-associated vesicle membrane;0.0146463956248649;74325!GO:0030658;transport vesicle membrane;0.0146463956248649;74325!GO:0030140;trans-Golgi network transport vesicle;0.0146463956248649;74325!GO:0030125;clathrin vesicle coat;0.0146463956248649;74325!GO:0030665;clathrin coated vesicle membrane;0.0147864159154189;74325!GO:0030133;transport vesicle;0.0157708802778738;74325!GO:0030120;vesicle coat;0.0183943176075133;74325!GO:0030662;coated vesicle membrane;0.0183943176075133;74325!GO:0005798;Golgi-associated vesicle;0.0183943176075133;74325!GO:0005905;coated pit;0.0187970422604788;74325!GO:0030118;clathrin coat;0.0191419569561835;74325!GO:0030659;cytoplasmic vesicle membrane;0.0199654984529125;74325!GO:0044433;cytoplasmic vesicle part;0.0227589329654743;74325!GO:0030117;membrane coat;0.0227589329654743;74325!GO:0048475;coated membrane;0.0227589329654743;74325!GO:0012506;vesicle membrane;0.0232170922115739;74325!GO:0000139;Golgi membrane;0.0271667427936787;74325!GO:0030136;clathrin-coated vesicle;0.0277441420857255;74325!GO:0030135;coated vesicle;0.0311243611438732;74325!GO:0006461;protein complex assembly;0.0427299765274537;74325!GO:0044431;Golgi apparatus part;0.0432344157632729;74325!GO:0008565;protein transporter 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|gostat_on_MCL_coexpression=GO:0030132;clathrin coat of coated pit;0.0146463956248649;74325!GO:0030130;clathrin coat of trans-Golgi network vesicle;0.0146463956248649;74325!GO:0012510;trans-Golgi network transport vesicle membrane;0.0146463956248649;74325!GO:0030660;Golgi-associated vesicle membrane;0.0146463956248649;74325!GO:0030658;transport vesicle membrane;0.0146463956248649;74325!GO:0030140;trans-Golgi network transport vesicle;0.0146463956248649;74325!GO:0030125;clathrin vesicle coat;0.0146463956248649;74325!GO:0030665;clathrin coated vesicle membrane;0.0147864159154189;74325!GO:0030133;transport vesicle;0.0157708802778738;74325!GO:0030120;vesicle coat;0.0183943176075133;74325!GO:0030662;coated vesicle membrane;0.0183943176075133;74325!GO:0005798;Golgi-associated vesicle;0.0183943176075133;74325!GO:0005905;coated pit;0.0187970422604788;74325!GO:0030118;clathrin coat;0.0191419569561835;74325!GO:0030659;cytoplasmic vesicle membrane;0.0199654984529125;74325!GO:0044433;cytoplasmic vesicle part;0.0227589329654743;74325!GO:0030117;membrane coat;0.0227589329654743;74325!GO:0048475;coated membrane;0.0227589329654743;74325!GO:0012506;vesicle membrane;0.0232170922115739;74325!GO:0000139;Golgi membrane;0.0271667427936787;74325!GO:0030136;clathrin-coated vesicle;0.0277441420857255;74325!GO:0030135;coated vesicle;0.0311243611438732;74325!GO:0006461;protein complex assembly;0.0427299765274537;74325!GO:0044431;Golgi apparatus part;0.0432344157632729;74325!GO:0008565;protein transporter activity;0.0449501943481015;74325!
|ontology_enrichment_celltype=CL:0002321!2.31e-13!70;CL:0000055!2.00e-08!49;CL:0000333!4.92e-08!10;CL:0000095!4.92e-08!10;CL:0000243!4.92e-08!10;CL:0000123!4.92e-08!10;CL:0000125!4.92e-08!10;CL:0000030!4.92e-08!10;CL:0000339!4.92e-08!10;CL:0000221!2.12e-07!44;CL:0000133!2.12e-07!44;CL:0002319!2.26e-07!43;CL:0000066!5.22e-07!25;CL:0002453!7.84e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!4.26e-17!95;UBERON:0000924!4.26e-17!95;UBERON:0006601!4.26e-17!95;UBERON:0001016!6.66e-16!75;UBERON:0001017!9.29e-15!73;UBERON:0000073!2.84e-14!54;UBERON:0001049!4.75e-13!52;UBERON:0005068!4.75e-13!52;UBERON:0006241!4.75e-13!52;UBERON:0007135!4.75e-13!52;UBERON:0010371!8.81e-12!73;UBERON:0002346!2.80e-11!64;UBERON:0003075!2.80e-11!64;UBERON:0007284!2.80e-11!64;UBERON:0000955!9.33e-11!47;UBERON:0006238!9.33e-11!47;UBERON:0002616!1.89e-10!46;UBERON:0011216!1.36e-09!194;UBERON:0000477!1.68e-09!244;UBERON:0002020!6.31e-09!34;UBERON:0010314!1.55e-08!92;UBERON:0003080!1.44e-07!40;UBERON:0004111!2.32e-07!122;UBERON:0003076!2.43e-07!12;UBERON:0003057!2.43e-07!12;UBERON:0002780!2.80e-07!39;UBERON:0001890!2.80e-07!39;UBERON:0006240!2.80e-07!39;UBERON:0003056!2.94e-07!49;UBERON:0003528!6.21e-07!29;UBERON:0002791!6.21e-07!29;UBERON:0001893!6.21e-07!29
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.876292,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,1.47707,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,1.23806,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.777706,1.44925,1.882,0.402065,0.411601,1.04436,1.20986,1.63704,0.476502,1.16055,1.00151,0.459035,1.32978,2.30787,0.568545,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,1.31639,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,2.74838,1.76245,1.38039,1.63982,0.876299,1.63327,0.580657,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,1.32874,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,3.0045,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
}}

Latest revision as of 19:11, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:54712670..54712687,-p3@Cltb
Mm9::chr13:54712693..54712748,-p1@Cltb
Mm9::chr2:164312019..164312155,+p1@Dbndd2


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:0030132clathrin coat of coated pit0.0146463956248649
GO:0030130clathrin coat of trans-Golgi network vesicle0.0146463956248649
GO:0012510trans-Golgi network transport vesicle membrane0.0146463956248649
GO:0030660Golgi-associated vesicle membrane0.0146463956248649
GO:0030658transport vesicle membrane0.0146463956248649
GO:0030140trans-Golgi network transport vesicle0.0146463956248649
GO:0030125clathrin vesicle coat0.0146463956248649
GO:0030665clathrin coated vesicle membrane0.0147864159154189
GO:0030133transport vesicle0.0157708802778738
GO:0030120vesicle coat0.0183943176075133
GO:0030662coated vesicle membrane0.0183943176075133
GO:0005798Golgi-associated vesicle0.0183943176075133
GO:0005905coated pit0.0187970422604788
GO:0030118clathrin coat0.0191419569561835
GO:0030659cytoplasmic vesicle membrane0.0199654984529125
GO:0044433cytoplasmic vesicle part0.0227589329654743
GO:0030117membrane coat0.0227589329654743
GO:0048475coated membrane0.0227589329654743
GO:0012506vesicle membrane0.0232170922115739
GO:0000139Golgi membrane0.0271667427936787
GO:0030136clathrin-coated vesicle0.0277441420857255
GO:0030135coated vesicle0.0311243611438732
GO:0006461protein complex assembly0.0427299765274537
GO:0044431Golgi apparatus part0.0432344157632729
GO:0008565protein transporter activity0.0449501943481015



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
ectoderm-derived structure4.26e-1795
ectoderm4.26e-1795
presumptive ectoderm4.26e-1795
nervous system6.66e-1675
central nervous system9.29e-1573
regional part of nervous system2.84e-1454
neural tube4.75e-1352
neural rod4.75e-1352
future spinal cord4.75e-1352
neural keel4.75e-1352
ecto-epithelium8.81e-1273
neurectoderm2.80e-1164
neural plate2.80e-1164
presumptive neural plate2.80e-1164
brain9.33e-1147
future brain9.33e-1147
regional part of brain1.89e-1046
organ system subdivision1.36e-09194
anatomical cluster1.68e-09244
gray matter6.31e-0934
structure with developmental contribution from neural crest1.55e-0892
anterior neural tube1.44e-0740
anatomical conduit2.32e-07122
posterior neural tube2.43e-0712
chordal neural plate2.43e-0712
regional part of forebrain2.80e-0739
forebrain2.80e-0739
future forebrain2.80e-0739
pre-chordal neural plate2.94e-0749
brain grey matter6.21e-0729
regional part of telencephalon6.21e-0729
telencephalon6.21e-0729


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)
MA0003.14.50747
MA0004.10.801718
MA0006.13.64748
MA0007.10.784593
MA0009.11.27673
MA0014.10.825079
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.932001
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.557057
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.11.7994
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.11.44606
MA0146.11.44443
MA0147.12.34772
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.22.07301
MA0138.21.07027
MA0002.20.466067
MA0137.21.60348
MA0104.21.21648
MA0047.20.962424
MA0112.20.794478
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.11.39671
MA0160.10.823568
MA0161.10
MA0162.17.41514
MA0163.13.6249
MA0164.10.933981
MA0080.20.64167
MA0018.22.17326
MA0099.21.06348
MA0079.21.4764
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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