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MCL coexpression mm9:366: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000485!2.98e-22!11;UBERON:0003350!3.48e-19!9;UBERON:0004808!3.48e-19!9;UBERON:0001277!3.48e-19!9;UBERON:0001242!1.26e-12!13;UBERON:0000060!1.26e-12!13;UBERON:0001262!1.26e-12!13;UBERON:0004786!1.26e-12!13;UBERON:0000344!1.15e-10!15
|ontology_enrichment_uberon=UBERON:0000485!2.98e-22!11;UBERON:0003350!3.48e-19!9;UBERON:0004808!3.48e-19!9;UBERON:0001277!3.48e-19!9;UBERON:0001242!1.26e-12!13;UBERON:0000060!1.26e-12!13;UBERON:0001262!1.26e-12!13;UBERON:0004786!1.26e-12!13;UBERON:0000344!1.15e-10!15
|tfbs_overrepresentation_for_novel_motifs=0.403818,0.534014,0.735588,0.15483,0.20878,0.164217,0.227275,0.103276,0.505464,0.243837,0.570169,0.623949,0.253571,0.665571,0.23002,0,0.38962,0.19894,0.429762,0.341948,0.310483,0.362751,0.664014,0.206855,0.755156,0.256873,0.209999,0.178177,0.0778495,0.74593,0.504259,0.476579,0.196184,0.874512,0.857292,0.0273756,0.0492863,0.617803,0.365025,0.304085,0.448825,0.512679,0.492213,0.0653594,0.33888,0.452134,0.323935,0.553328,0.243974,0.272179,0.374992,0.760562,0.129123,0.603398,0.619345,0.677917,0.284478,1.13518,0.378245,0.240064,0.459084,0.777251,0.543433,0.365621,0.2499,1.03267,0.745869,1.08074,0.455021,0.938231,0.687161,0.792871,0.124062,0.650163,0.0701313,0.551953,0.176178,0.314806,0.444191,0.0954455,0.266969,0.404291,0.283653,0.45564,0.545133,0.85634,0.246689,0.746706,1.57343,1.23935,0.811671,0.549603,0.487824,0.216228,0.0396727,0.580811,0.100987,0.490297,1.56012,0.108849,0.185028,0.476334,1.43493,0.375488,0.374608,0.511961,1.08837,0.186164,0.0980442,0.31304,0.393011,0.58915,0.0960466,0.199544,0.818358,0.444691,0.0170916,0.157255,0.390716,0.180519,0.655146,0.348339,0.258253,0.314081,0.869916,0.447391,0.233251,0.481866,0.744444,0.827806,0.572132,0.458245,0.716744,0.251791,0.838892,0.0456113,0.416802,0.514981,0.792231,1.60311,1.2081,0.750296,0.267427,0.48577,0.369214,0.988409,0.326451,1.56378,0.420463,0.210988,0.497376,0.0380342,0.60483,0.14223,0.699993,0.680035,0.278231,0.245756,0.127194,0.416368,0.801233,0.544365,0.447776,0.123129,0.366469,0.245542,0.183595,0.217399,2.17439
|tfbs_overrepresentation_for_novel_motifs=0.403818,0.534014,0.735588,0.15483,0.20878,0.164217,0.227275,0.103276,0.505464,0.243837,0.570169,0.623949,0.253571,0.665571,0.23002,0,0.38962,0.19894,0.429762,0.341948,0.310483,0.362751,0.664014,0.206855,0.755156,0.256873,0.209999,0.178177,0.0778495,0.74593,0.504259,0.476579,0.196184,0.874512,0.857292,0.0273756,0.0492863,0.617803,0.365025,0.304085,0.448825,0.512679,0.492213,0.0653594,0.33888,0.452134,0.323935,0.553328,0.243974,0.272179,0.374992,0.760562,0.129123,0.603398,0.619345,0.677917,0.284478,1.13518,0.378245,0.240064,0.459084,0.777251,0.543433,0.365621,0.2499,1.03267,0.745869,1.08074,0.455021,0.938231,0.687161,0.792871,0.124062,0.650163,0.0701313,0.551953,0.176178,0.314806,0.444191,0.0954455,0.266969,0.404291,0.283653,0.45564,0.545133,0.85634,0.246689,0.746706,1.57343,1.23935,0.811671,0.549603,0.487824,0.216228,0.0396727,0.580811,0.100987,0.490297,1.56012,0.108849,0.185028,0.476334,1.43493,0.375488,0.374608,0.511961,1.08837,0.186164,0.0980442,0.31304,0.393011,0.58915,0.0960466,0.199544,0.818358,0.444691,0.0170916,0.157255,0.390716,0.180519,0.655146,0.348339,0.258253,0.314081,0.869916,0.447391,0.233251,0.481866,0.744444,0.827806,0.572132,0.458245,0.716744,0.251791,0.838892,0.0456113,0.416802,0.514981,0.792231,1.60311,1.2081,0.750296,0.267427,0.48577,0.369214,0.988409,0.326451,1.56378,0.420463,0.210988,0.497376,0.0380342,0.60483,0.14223,0.699993,0.680035,0.278231,0.245756,0.127194,0.416368,0.801233,0.544365,0.447776,0.123129,0.366469,0.245542,0.183595,0.217399,2.17439
|tfbs_overrepresentation_jaspar=MA0003.1;0.110225,MA0004.1;2.10701,MA0006.1;0.839827,MA0007.1;0.446853,MA0009.1;0.499857,MA0014.1;0.643452,MA0017.1;0.259254,MA0019.1;0.344318,MA0024.1;1.1668,MA0025.1;1.69601,MA0027.1;2.09948,MA0028.1;1.83592,MA0029.1;0.442582,MA0030.1;0.448261,MA0031.1;0.417663,MA0038.1;0.256813,MA0040.1;0.510947,MA0041.1;0.109446,MA0042.1;0.334544,MA0043.1;1.43301,MA0046.1;0.531807,MA0048.1;0.233057,MA0050.1;0.533529,MA0051.1;0.263603,MA0052.1;1.28806,MA0055.1;0.0107959,MA0056.1;0,MA0057.1;0.577065,MA0058.1;2.88175,MA0059.1;0.698078,MA0060.1;1.28316,MA0061.1;1.46405,MA0063.1;0,MA0066.1;1.98696,MA0067.1;0.817149,MA0068.1;1.5357,MA0069.1;0.518414,MA0070.1;0.509795,MA0071.1;0.532153,MA0072.1;0.502282,MA0073.1;0.74267,MA0074.1;0.632353,MA0076.1;1.49392,MA0077.1;0.48317,MA0078.1;0.78707,MA0081.1;0.37696,MA0083.1;0.585897,MA0084.1;1.1333,MA0087.1;0.546952,MA0088.1;0.376174,MA0089.1;0,MA0090.1;0.416778,MA0091.1;0.491727,MA0092.1;0.417266,MA0093.1;3.11214,MA0095.1;0,MA0098.1;0,MA0100.1;0.612698,MA0101.1;0.355777,MA0103.1;0.273906,MA0105.1;2.00986,MA0106.1;0.295186,MA0107.1;0.952044,MA0108.2;0.363107,MA0109.1;0,MA0111.1;0.863236,MA0113.1;0.750951,MA0114.1;0.160582,MA0115.1;0.589161,MA0116.1;0.486423,MA0117.1;0.559943,MA0119.1;0.110503,MA0122.1;0.577888,MA0124.1;0.766819,MA0125.1;0.697415,MA0130.1;0,MA0131.1;0.340612,MA0132.1;0,MA0133.1;0,MA0135.1;0.619844,MA0136.1;0.236653,MA0139.1;0.245643,MA0140.1;0.2137,MA0141.1;1.04657,MA0142.1;0.40532,MA0143.1;0.285913,MA0144.1;0.666779,MA0145.1;0.625223,MA0146.1;1.53473,MA0147.1;0.400991,MA0148.1;0.165681,MA0149.1;0.113293,MA0062.2;1.62311,MA0035.2;0.620478,MA0039.2;7.05432,MA0138.2;0.334152,MA0002.2;0.251244,MA0137.2;0.297219,MA0104.2;1.19869,MA0047.2;0.711867,MA0112.2;0.625195,MA0065.2;0.627676,MA0150.1;0.145553,MA0151.1;0,MA0152.1;0.712054,MA0153.1;0.635107,MA0154.1;0.400841,MA0155.1;0.164369,MA0156.1;0.59518,MA0157.1;0.378326,MA0158.1;0,MA0159.1;0.423802,MA0160.1;0.968677,MA0161.1;0,MA0162.1;1.19439,MA0163.1;0.228582,MA0164.1;0.667063,MA0080.2;0.0773362,MA0018.2;0.244112,MA0099.2;0.329046,MA0079.2;1.50282,MA0102.2;1.18455,MA0258.1;0.610753,MA0259.1;1.47814,MA0442.1;0
}}
}}

Revision as of 11:38, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:61142788..61142812,-p@chr10:61142788..61142812
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Mm9::chr11:120210728..120210741,-p@chr11:120210728..120210741
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Mm9::chr11:69231755..69231768,+p@chr11:69231755..69231768
+
Mm9::chr11:70034726..70034742,+p@chr11:70034726..70034742
+
Mm9::chr12:40950158..40950203,+p@chr12:40950158..40950203
+
Mm9::chr13:64255017..64255028,+p@chr13:64255017..64255028
+
Mm9::chr15:79158013..79158024,+p@chr15:79158013..79158024
+
Mm9::chr15:85465336..85465350,+p@chr15:85465336..85465350
+
Mm9::chr16:30064250..30064282,+p6@Hes1
Mm9::chr18:6136418..6136425,+p@chr18:6136418..6136425
+
Mm9::chr1:174430288..174430293,-p@chr1:174430288..174430293
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Mm9::chr1:90966570..90966579,-p@chr1:90966570..90966579
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Mm9::chr3:131067652..131067658,-p@chr3:131067652..131067658
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Mm9::chr4:134409493..134409529,+p@chr4:134409493..134409529
+
Mm9::chr6:48504716..48504730,-p@chr6:48504716..48504730
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Mm9::chr7:117308382..117308389,-p@chr7:117308382..117308389
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Mm9::chr7:19912585..19912612,-p@chr7:19912585..19912612
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Mm9::chr7:26540490..26540493,+p@chr7:26540490..26540493
+
Mm9::chr7:52105222..52105237,-p@chr7:52105222..52105237
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Mm9::chr8:73222216..73222226,-p@chr8:73222216..73222226
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Mm9::chrX:71211824..71211845,+p@chrX:71211824..71211845
+


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:0045608negative regulation of auditory receptor cell differentiation0.00258274569346722
GO:0045605negative regulation of epidermal cell differentiation0.00258274569346722
GO:0045632negative regulation of mechanoreceptor differentiation0.00258274569346722
GO:0045683negative regulation of epidermis development0.00258274569346722
GO:0042668auditory receptor cell fate determination0.00258274569346722
GO:0045607regulation of auditory receptor cell differentiation0.00258274569346722
GO:0045631regulation of mechanoreceptor differentiation0.00258274569346722
GO:0009912auditory receptor cell fate commitment0.00273927573549553
GO:0048505regulation of timing of cell differentiation0.00273927573549553
GO:0040034regulation of development, heterochronic0.00273927573549553
GO:0060120inner ear receptor cell fate commitment0.00273927573549553
GO:0045604regulation of epidermal cell differentiation0.00301320330904509
GO:0045682regulation of epidermis development0.00370855791882473
GO:0045665negative regulation of neuron differentiation0.00688732184924592
GO:0021983pituitary gland development0.00723168794170821
GO:0021536diencephalon development0.0074443846458761
GO:0001889liver development0.0074443846458761
GO:0042491auditory receptor cell differentiation0.00761230309653496
GO:0001709cell fate determination0.00761230309653496
GO:0045664regulation of neuron differentiation0.00774823708040166
GO:0060113inner ear receptor cell differentiation0.00774823708040166
GO:0042490mechanoreceptor differentiation0.00903960992713526
GO:0009913epidermal cell differentiation0.00917061876665896
GO:0035270endocrine system development0.0118117569714568
GO:0048730epidermis morphogenesis0.0118117569714568
GO:0030324lung development0.0143127157179642
GO:0030323respiratory tube development0.0143127157179642
GO:0048839inner ear development0.0143127157179642
GO:0048732gland development0.0143127157179642
GO:0048469cell maturation0.0143127157179642
GO:0048729tissue morphogenesis0.0143127157179642
GO:0043583ear development0.0143127157179642
GO:0045596negative regulation of cell differentiation0.0155225625011414
GO:0021700developmental maturation0.0160175544322923
GO:0008544epidermis development0.0160175544322923
GO:0030900forebrain development0.0160175544322923
GO:0045165cell fate commitment0.0160175544322923
GO:0007398ectoderm development0.0160175544322923
GO:0051093negative regulation of developmental process0.0160704176482405
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0210924231633156
GO:0045595regulation of cell differentiation0.0219533383944714
GO:0016564transcription repressor activity0.0219533383944714
GO:0008284positive regulation of cell proliferation0.0244986529909318
GO:0007420brain development0.0244986529909318
GO:0007423sensory organ development0.0244986529909318
GO:0045892negative regulation of transcription, DNA-dependent0.0244986529909318
GO:0035295tube development0.025772504898641
GO:0007417central nervous system development0.029002081849559
GO:0016481negative regulation of transcription0.0292711178592952
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0302501979260997
GO:0050793regulation of developmental process0.0302501979260997
GO:0030182neuron differentiation0.0319513256544026
GO:0009888tissue development0.0319513256544026
GO:0031324negative regulation of cellular metabolic process0.0325872357867099
GO:0048699generation of neurons0.0341137660345462
GO:0042127regulation of cell proliferation0.0341137660345462
GO:0009892negative regulation of metabolic process0.0348897225257852
GO:0022008neurogenesis0.0351194040847324
GO:0006357regulation of transcription from RNA polymerase II promoter0.0388141443199028
GO:0006366transcription from RNA polymerase II promoter0.0422852864369327
GO:0008283cell proliferation0.0456426206156994
GO:0009887organ morphogenesis0.0484056531582082



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
simple columnar epithelium2.98e-2211
epithelium of mucosa3.48e-199
gastrointestinal system epithelium3.48e-199
intestinal epithelium3.48e-199
intestinal mucosa1.26e-1213
anatomical wall1.26e-1213
wall of intestine1.26e-1213
gastrointestinal system mucosa1.26e-1213
mucosa1.15e-1015


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)
MA0003.10.110225
MA0004.12.10701
MA0006.10.839827
MA0007.10.446853
MA0009.10.499857
MA0014.10.643452
MA0017.10.259254
MA0019.10.344318
MA0024.11.1668
MA0025.11.69601
MA0027.12.09948
MA0028.11.83592
MA0029.10.442582
MA0030.10.448261
MA0031.10.417663
MA0038.10.256813
MA0040.10.510947
MA0041.10.109446
MA0042.10.334544
MA0043.11.43301
MA0046.10.531807
MA0048.10.233057
MA0050.10.533529
MA0051.10.263603
MA0052.11.28806
MA0055.10.0107959
MA0056.10
MA0057.10.577065
MA0058.12.88175
MA0059.10.698078
MA0060.11.28316
MA0061.11.46405
MA0063.10
MA0066.11.98696
MA0067.10.817149
MA0068.11.5357
MA0069.10.518414
MA0070.10.509795
MA0071.10.532153
MA0072.10.502282
MA0073.10.74267
MA0074.10.632353
MA0076.11.49392
MA0077.10.48317
MA0078.10.78707
MA0081.10.37696
MA0083.10.585897
MA0084.11.1333
MA0087.10.546952
MA0088.10.376174
MA0089.10
MA0090.10.416778
MA0091.10.491727
MA0092.10.417266
MA0093.13.11214
MA0095.10
MA0098.10
MA0100.10.612698
MA0101.10.355777
MA0103.10.273906
MA0105.12.00986
MA0106.10.295186
MA0107.10.952044
MA0108.20.363107
MA0109.10
MA0111.10.863236
MA0113.10.750951
MA0114.10.160582
MA0115.10.589161
MA0116.10.486423
MA0117.10.559943
MA0119.10.110503
MA0122.10.577888
MA0124.10.766819
MA0125.10.697415
MA0130.10
MA0131.10.340612
MA0132.10
MA0133.10
MA0135.10.619844
MA0136.10.236653
MA0139.10.245643
MA0140.10.2137
MA0141.11.04657
MA0142.10.40532
MA0143.10.285913
MA0144.10.666779
MA0145.10.625223
MA0146.11.53473
MA0147.10.400991
MA0148.10.165681
MA0149.10.113293
MA0062.21.62311
MA0035.20.620478
MA0039.27.05432
MA0138.20.334152
MA0002.20.251244
MA0137.20.297219
MA0104.21.19869
MA0047.20.711867
MA0112.20.625195
MA0065.20.627676
MA0150.10.145553
MA0151.10
MA0152.10.712054
MA0153.10.635107
MA0154.10.400841
MA0155.10.164369
MA0156.10.59518
MA0157.10.378326
MA0158.10
MA0159.10.423802
MA0160.10.968677
MA0161.10
MA0162.11.19439
MA0163.10.228582
MA0164.10.667063
MA0080.20.0773362
MA0018.20.244112
MA0099.20.329046
MA0079.21.50282
MA0102.21.18455
MA0258.10.610753
MA0259.11.47814
MA0442.10
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