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MCL coexpression mm9:2102: Difference between revisions

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{{MCL_coexpression_mm9
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regulation of oligodendrocyte differentiation;0.00854560379022112;382867!GO:0048713;regulation of oligodendrocyte differentiation;0.00854560379022112;382867!GO:0014015;positive regulation of gliogenesis;0.00854560379022112;382867!GO:0045687;positive regulation of glial cell differentiation;0.00854560379022112;382867!GO:0014003;oligodendrocyte development;0.00854560379022112;382867!GO:0045685;regulation of glial cell differentiation;0.00949381462173878;382867!GO:0014013;regulation of gliogenesis;0.00949381462173878;382867!GO:0048709;oligodendrocyte differentiation;0.00949381462173878;382867!GO:0021782;glial cell development;0.00949381462173878;382867!GO:0010001;glial cell differentiation;0.0318203804753961;382867!GO:0042063;gliogenesis;0.0318203804753961;382867!GO:0045597;positive regulation of cell differentiation;0.0327213510388878;382867!GO:0051094;positive regulation of developmental 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|gostat_on_MCL_coexpression=GO:0048714;positive regulation of oligodendrocyte differentiation;0.00854560379022112;382867!GO:0048713;regulation of oligodendrocyte differentiation;0.00854560379022112;382867!GO:0014015;positive regulation of gliogenesis;0.00854560379022112;382867!GO:0045687;positive regulation of glial cell differentiation;0.00854560379022112;382867!GO:0014003;oligodendrocyte development;0.00854560379022112;382867!GO:0045685;regulation of glial cell differentiation;0.00949381462173878;382867!GO:0014013;regulation of gliogenesis;0.00949381462173878;382867!GO:0048709;oligodendrocyte differentiation;0.00949381462173878;382867!GO:0021782;glial cell development;0.00949381462173878;382867!GO:0010001;glial cell differentiation;0.0318203804753961;382867!GO:0042063;gliogenesis;0.0318203804753961;382867!GO:0045597;positive regulation of cell differentiation;0.0327213510388878;382867!GO:0051094;positive regulation of developmental process;0.0452779046561311;382867!
|ontology_enrichment_celltype=CL:0000540!1.12e-10!33;CL:0000047!1.12e-10!33;CL:0000031!1.12e-10!33;CL:0000404!1.12e-10!33;CL:0000107!5.37e-08!9;CL:0000221!5.42e-08!44;CL:0000133!5.42e-08!44;CL:0002319!5.61e-08!43;CL:0000393!3.56e-07!39;CL:0000211!3.56e-07!39
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|ontology_enrichment_uberon=UBERON:0004121!1.08e-23!95;UBERON:0000924!1.08e-23!95;UBERON:0006601!1.08e-23!95;UBERON:0001016!3.21e-20!75;UBERON:0001017!4.48e-20!73;UBERON:0002346!1.54e-19!64;UBERON:0003075!1.54e-19!64;UBERON:0007284!1.54e-19!64;UBERON:0010371!6.50e-18!73;UBERON:0003056!2.12e-13!49;UBERON:0010314!2.15e-13!92;UBERON:0000073!6.41e-13!54;UBERON:0001049!6.85e-12!52;UBERON:0005068!6.85e-12!52;UBERON:0006241!6.85e-12!52;UBERON:0007135!6.85e-12!52;UBERON:0000955!1.84e-09!47;UBERON:0006238!1.84e-09!47;UBERON:0002616!5.20e-09!46;UBERON:0002020!7.36e-09!34;UBERON:0003080!2.95e-08!40;UBERON:0002410!5.37e-08!9;UBERON:0002780!9.00e-08!39;UBERON:0001890!9.00e-08!39;UBERON:0006240!9.00e-08!39;UBERON:0000010!1.46e-07!11;UBERON:0000970!2.32e-07!9;UBERON:0000019!2.32e-07!9;UBERON:0000047!2.32e-07!9;UBERON:0010312!2.32e-07!9;UBERON:0004088!2.32e-07!9;UBERON:0002104!2.32e-07!9;UBERON:0001456!2.32e-07!9;UBERON:0003072!2.32e-07!9;UBERON:0004128!2.32e-07!9;UBERON:0003071!2.32e-07!9
|tfbs_overrepresentation_for_novel_motifs=1.54788,0.128156,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,2.59282,0.81685,0.502646,0,1.02248,1.19379,0.352304,0.683591,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,1.44018,0.711848,1.12823,0.471365,0.854272,0.503207,1.04375,0.460474,0.786577,1.10929,0.40068,0.478558,0.717547,0.185353,1.26006,0.325217,1.61988,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,1.44172,0.377213,0.593145,1.32691,0.323563,1.50994,0.318792,3.51623,1.08947,0.575233,0.986898,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,1.4408,0.943446,1.94914,1.50286,1.21342,1.14153,1.22838,0.430015,1.05366,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,1.42067,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.442329,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,1.90229,1.13449,1.43038,1.2358,1.23918,0.680176,1.40022,3.24627,1.53196,1.08088,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.992915
|tfbs_overrepresentation_jaspar=MA0003.1;0.942378,MA0004.1;0.6888,MA0006.1;1.24418,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.276754,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.735223,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;1.29714,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.00221226,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.201215,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.957842,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.21199,MA0146.1;1.07887,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;1.07321,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;0.650923,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.346529,MA0163.1;0.327769,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.612404,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 18:00, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:34791937..34791977,-p1@Zfp488
Mm9::chr14:34791987..34791998,-p2@Zfp488
Mm9::chr7:38554745..38554756,-p7@Zfp536
Mm9::chr7:38554763..38554780,-p1@Zfp536


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:0048714positive regulation of oligodendrocyte differentiation0.00854560379022112
GO:0048713regulation of oligodendrocyte differentiation0.00854560379022112
GO:0014015positive regulation of gliogenesis0.00854560379022112
GO:0045687positive regulation of glial cell differentiation0.00854560379022112
GO:0014003oligodendrocyte development0.00854560379022112
GO:0045685regulation of glial cell differentiation0.00949381462173878
GO:0014013regulation of gliogenesis0.00949381462173878
GO:0048709oligodendrocyte differentiation0.00949381462173878
GO:0021782glial cell development0.00949381462173878
GO:0010001glial cell differentiation0.0318203804753961
GO:0042063gliogenesis0.0318203804753961
GO:0045597positive regulation of cell differentiation0.0327213510388878
GO:0051094positive regulation of developmental process0.0452779046561311



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
neuron1.12e-1033
neuronal stem cell1.12e-1033
neuroblast1.12e-1033
electrically signaling cell1.12e-1033
autonomic neuron5.37e-089
ectodermal cell5.42e-0844
neurectodermal cell5.42e-0844
neural cell5.61e-0843
electrically responsive cell3.56e-0739
electrically active cell3.56e-0739

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.08e-2395
ectoderm1.08e-2395
presumptive ectoderm1.08e-2395
nervous system3.21e-2075
central nervous system4.48e-2073
neurectoderm1.54e-1964
neural plate1.54e-1964
presumptive neural plate1.54e-1964
ecto-epithelium6.50e-1873
pre-chordal neural plate2.12e-1349
structure with developmental contribution from neural crest2.15e-1392
regional part of nervous system6.41e-1354
neural tube6.85e-1252
neural rod6.85e-1252
future spinal cord6.85e-1252
neural keel6.85e-1252
brain1.84e-0947
future brain1.84e-0947
regional part of brain5.20e-0946
gray matter7.36e-0934
anterior neural tube2.95e-0840
autonomic nervous system5.37e-089
regional part of forebrain9.00e-0839
forebrain9.00e-0839
future forebrain9.00e-0839
peripheral nervous system1.46e-0711
eye2.32e-079
camera-type eye2.32e-079
simple eye2.32e-079
immature eye2.32e-079
ocular region2.32e-079
visual system2.32e-079
face2.32e-079
optic cup2.32e-079
optic vesicle2.32e-079
eye primordium2.32e-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)
MA0003.10.942378
MA0004.10.6888
MA0006.11.24418
MA0007.10.672186
MA0009.11.15569
MA0014.10.276754
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.735223
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.11.29714
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.00221226
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.957842
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.21199
MA0146.11.07887
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.21.07321
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.346529
MA0163.10.327769
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.612404
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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