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MCL coexpression mm9:507: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004122!1.10e-11!5;UBERON:0000080!8.19e-10!4;UBERON:0005904!8.19e-10!4;UBERON:0006947!8.19e-10!4;UBERON:0002120!8.19e-10!4;UBERON:0004054!8.19e-10!4;UBERON:0004875!8.19e-10!4;UBERON:0004876!8.19e-10!4;UBERON:0005721!8.19e-10!4;UBERON:0005754!8.19e-10!4;UBERON:0007297!8.19e-10!4;UBERON:0005156!9.47e-10!26;UBERON:0000990!9.47e-10!26;UBERON:0004175!6.82e-09!9;UBERON:0001008!7.56e-08!19;UBERON:0000161!7.88e-08!5;UBERON:0000162!9.11e-08!3;UBERON:0001353!9.11e-08!3;UBERON:0000163!9.11e-08!3;UBERON:0006866!9.11e-08!3;UBERON:0001046!9.11e-08!3;UBERON:0000164!9.11e-08!3;UBERON:0000931!9.11e-08!3;UBERON:0003101!9.69e-08!16;UBERON:0000079!9.69e-08!16;UBERON:0001301!1.11e-07!3;UBERON:0006555!1.11e-07!3;UBERON:0005103!1.11e-07!3;UBERON:0000083!1.11e-07!3;UBERON:0009201!1.11e-07!3;UBERON:0004819!1.11e-07!3;UBERON:0006553!1.11e-07!3;UBERON:0003074!1.11e-07!3;UBERON:0003060!1.11e-07!3;UBERON:0003064!2.54e-07!14;UBERON:0003133!3.10e-07!24
|ontology_enrichment_uberon=UBERON:0004122!1.10e-11!5;UBERON:0000080!8.19e-10!4;UBERON:0005904!8.19e-10!4;UBERON:0006947!8.19e-10!4;UBERON:0002120!8.19e-10!4;UBERON:0004054!8.19e-10!4;UBERON:0004875!8.19e-10!4;UBERON:0004876!8.19e-10!4;UBERON:0005721!8.19e-10!4;UBERON:0005754!8.19e-10!4;UBERON:0007297!8.19e-10!4;UBERON:0005156!9.47e-10!26;UBERON:0000990!9.47e-10!26;UBERON:0004175!6.82e-09!9;UBERON:0001008!7.56e-08!19;UBERON:0000161!7.88e-08!5;UBERON:0000162!9.11e-08!3;UBERON:0001353!9.11e-08!3;UBERON:0000163!9.11e-08!3;UBERON:0006866!9.11e-08!3;UBERON:0001046!9.11e-08!3;UBERON:0000164!9.11e-08!3;UBERON:0000931!9.11e-08!3;UBERON:0003101!9.69e-08!16;UBERON:0000079!9.69e-08!16;UBERON:0001301!1.11e-07!3;UBERON:0006555!1.11e-07!3;UBERON:0005103!1.11e-07!3;UBERON:0000083!1.11e-07!3;UBERON:0009201!1.11e-07!3;UBERON:0004819!1.11e-07!3;UBERON:0006553!1.11e-07!3;UBERON:0003074!1.11e-07!3;UBERON:0003060!1.11e-07!3;UBERON:0003064!2.54e-07!14;UBERON:0003133!3.10e-07!24
|tfbs_overrepresentation_for_novel_motifs=0.224466,0.954724,0.204219,0.716126,0.391122,0.269875,0.346405,0.875434,0.0719629,0.112618,0.308886,0.336042,0.0670839,0.357027,0.830717,0,0.530547,0.118546,0.814719,0.465097,0.176628,0.837419,0.356242,0.77745,0.210021,0.381085,0.448115,0.782755,0.154744,0.611262,0.275529,0.624931,0.117091,0.397142,0.135203,0.271144,0.111136,0.332941,0.662669,0.0808072,0.384293,0.279796,1.45268,0.423138,1.23768,0.24907,0.457618,0.300372,0.237017,0.92391,0.514446,1.04423,0.584697,0.759566,0.776306,0.363247,0.163199,0.325117,0.744745,0.36147,0.606104,0.413233,0.569343,0.504093,0.372973,0.541429,0.908031,1.25063,0.60172,1.10561,0.189925,0.0700673,0.0681764,0.808562,0.181606,0.166516,0.17621,0.447339,0.590017,0.179738,0.530081,1.34858,0.411949,0.227715,0.69807,0.0177525,0.0223411,0.145915,0.462057,1.41118,0.975915,0.702809,0.636995,0.127646,0.651159,0.287636,0.503836,0.639644,0.457849,0.0288834,0.111186,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.804983,1.03226,0.177945,1.17217,0.744577,0.180573,0.313258,0.982794,0.381263,0.0290103,0.723174,0.53175,1.17709,0.813766,0.484912,0.995764,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,0.129636,0.726634,0.702495,0.877862,1.7391,1.0039,0.323891,0.65343,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,1.40165,0.460443,1.73788,2.67359,0.124893,0.148959,0.144255,0.761071,0.618088,0.374365,0.839715,0.405736,0.143092,0.633366,0.230865,0.96517,0.697256,0.593895,0.21719,0.50503,0.367885,0.110426,0.33468,0.00671205
|tfbs_overrepresentation_for_novel_motifs=0.224466,0.954724,0.204219,0.716126,0.391122,0.269875,0.346405,0.875434,0.0719629,0.112618,0.308886,0.336042,0.0670839,0.357027,0.830717,0,0.530547,0.118546,0.814719,0.465097,0.176628,0.837419,0.356242,0.77745,0.210021,0.381085,0.448115,0.782755,0.154744,0.611262,0.275529,0.624931,0.117091,0.397142,0.135203,0.271144,0.111136,0.332941,0.662669,0.0808072,0.384293,0.279796,1.45268,0.423138,1.23768,0.24907,0.457618,0.300372,0.237017,0.92391,0.514446,1.04423,0.584697,0.759566,0.776306,0.363247,0.163199,0.325117,0.744745,0.36147,0.606104,0.413233,0.569343,0.504093,0.372973,0.541429,0.908031,1.25063,0.60172,1.10561,0.189925,0.0700673,0.0681764,0.808562,0.181606,0.166516,0.17621,0.447339,0.590017,0.179738,0.530081,1.34858,0.411949,0.227715,0.69807,0.0177525,0.0223411,0.145915,0.462057,1.41118,0.975915,0.702809,0.636995,0.127646,0.651159,0.287636,0.503836,0.639644,0.457849,0.0288834,0.111186,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.804983,1.03226,0.177945,1.17217,0.744577,0.180573,0.313258,0.982794,0.381263,0.0290103,0.723174,0.53175,1.17709,0.813766,0.484912,0.995764,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,0.129636,0.726634,0.702495,0.877862,1.7391,1.0039,0.323891,0.65343,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,1.40165,0.460443,1.73788,2.67359,0.124893,0.148959,0.144255,0.761071,0.618088,0.374365,0.839715,0.405736,0.143092,0.633366,0.230865,0.96517,0.697256,0.593895,0.21719,0.50503,0.367885,0.110426,0.33468,0.00671205
|tfbs_overrepresentation_jaspar=MA0003.1;0.056804,MA0004.1;0.717031,MA0006.1;0.1319,MA0007.1;0.246385,MA0009.1;0.649874,MA0014.1;0.0625332,MA0017.1;0.895796,MA0019.1;0.480432,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;0.138956,MA0029.1;0.588275,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;0.661716,MA0041.1;0.577334,MA0042.1;0.189008,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;0.0293065,MA0050.1;0.789929,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;0.276048,MA0056.1;0,MA0057.1;0.107353,MA0058.1;0.541281,MA0059.1;0.563468,MA0060.1;0.0819399,MA0061.1;1.11472,MA0063.1;0,MA0066.1;1.72598,MA0067.1;0.981551,MA0068.1;0.271058,MA0069.1;1.60692,MA0070.1;0.660488,MA0071.1;0.289658,MA0072.1;0.652465,MA0073.1;0.0195439,MA0074.1;0.902074,MA0076.1;0.163664,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;0.210747,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.339729,MA0089.1;0,MA0090.1;0.231074,MA0091.1;0.269175,MA0092.1;0.231323,MA0093.1;0.444403,MA0095.1;0,MA0098.1;0,MA0100.1;0.879972,MA0101.1;1.72541,MA0103.1;0.157724,MA0105.1;0.385363,MA0106.1;0.425111,MA0107.1;1.45792,MA0108.2;0.50131,MA0109.1;0,MA0111.1;1.26116,MA0113.1;1.03368,MA0114.1;1.10492,MA0115.1;0.744589,MA0116.1;0.131762,MA0117.1;0.713754,MA0119.1;0.580747,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;0.77683,MA0136.1;0.357464,MA0139.1;0.231431,MA0140.1;0.330266,MA0141.1;0.511953,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;1.64479,MA0145.1;0.189432,MA0146.1;0.0343188,MA0147.1;0.349075,MA0148.1;0.747422,MA0149.1;0.204102,MA0062.2;0.046824,MA0035.2;1.5961,MA0039.2;0.218113,MA0138.2;0.469076,MA0002.2;0.0664561,MA0137.2;2.9583,MA0104.2;0.257564,MA0047.2;0.380343,MA0112.2;0.370361,MA0065.2;0.371748,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.380437,MA0153.1;0.792819,MA0154.1;0.283993,MA0155.1;0.22104,MA0156.1;0.490212,MA0157.1;1.28808,MA0158.1;0,MA0159.1;0.114033,MA0160.1;0.274172,MA0161.1;0,MA0162.1;0.0134677,MA0163.1;0.0112325,MA0164.1;0.357779,MA0080.2;0.467794,MA0018.2;0.366212,MA0099.2;0.463355,MA0079.2;0.00214241,MA0102.2;1.35579,MA0258.1;0.0900907,MA0259.1;0.331447,MA0442.1;0
}}
}}

Revision as of 11:52, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127470688..127470731,+p@chr10:127470688..127470731
+
Mm9::chr14:63585020..63585025,-p@chr14:63585020..63585025
-
Mm9::chr14:63585028..63585037,-p@chr14:63585028..63585037
-
Mm9::chr14:63585048..63585062,-p@chr14:63585048..63585062
-
Mm9::chr15:37163047..37163087,-p1@ENSMUST00000160264
Mm9::chr15:85476119..85476143,+p2@uc007xdi.1
Mm9::chr18:44413512..44413521,-p@chr18:44413512..44413521
-
Mm9::chr1:155964760..155964772,-p1@uc007das.1
Mm9::chr3:146444177..146444215,-p@chr3:146444177..146444215
-
Mm9::chr4:46614213..46614246,+p@chr4:46614213..46614246
+
Mm9::chr4:61941433..61941455,+p@chr4:61941433..61941455
+
Mm9::chr7:116781120..116781134,-p@chr7:116781120..116781134
-
Mm9::chr7:135148666..135148682,-p1@ENSMUST00000126205
Mm9::chrX:105011839..105011859,+p2@Fam46d


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:0004691cAMP-dependent protein kinase activity0.00602640661809018
GO:0004690cyclic nucleotide-dependent protein kinase activity0.00602640661809018
GO:0005952cAMP-dependent protein kinase complex0.00903960992713527
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0271188297814058
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0271188297814058
GO:0019933cAMP-mediated signaling0.0271188297814058
GO:0019935cyclic-nucleotide-mediated signaling0.0271188297814058
GO:0019932second-messenger-mediated signaling0.0463280008765682



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
genitourinary system1.10e-115
mesonephros8.19e-104
duct of male reproductive system8.19e-104
male genital duct8.19e-104
pronephros8.19e-104
internal male genitalia8.19e-104
nephrogenic cord8.19e-104
urogenital ridge8.19e-104
pronephric mesoderm8.19e-104
rostral part of nephrogenic cord8.19e-104
presumptive pronephric mesoderm8.19e-104
reproductive structure9.47e-1026
reproductive system9.47e-1026
internal genitalia6.82e-099
renal system7.56e-0819
orifice7.88e-085
cloaca9.11e-083
anal region9.11e-083
embryonic cloaca9.11e-083
terminal part of digestive tract9.11e-083
hindgut9.11e-083
primitive urogenital sinus9.11e-083
proctodeum9.11e-083
male organism9.69e-0816
male reproductive system9.69e-0816
epididymis1.11e-073
excretory tube1.11e-073
mesonephric epithelium1.11e-073
mesonephric tubule1.11e-073
nephric duct1.11e-073
kidney epithelium1.11e-073
renal duct1.11e-073
mesonephric duct1.11e-073
pronephric duct1.11e-073
intermediate mesoderm2.54e-0714
reproductive organ3.10e-0724


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)
MA0003.10.056804
MA0004.10.717031
MA0006.10.1319
MA0007.10.246385
MA0009.10.649874
MA0014.10.0625332
MA0017.10.895796
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.138956
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.577334
MA0042.10.189008
MA0043.10.74191
MA0046.10.683926
MA0048.10.0293065
MA0050.10.789929
MA0051.10.388883
MA0052.10.669354
MA0055.10.276048
MA0056.10
MA0057.10.107353
MA0058.10.541281
MA0059.10.563468
MA0060.10.0819399
MA0061.11.11472
MA0063.10
MA0066.11.72598
MA0067.10.981551
MA0068.10.271058
MA0069.11.60692
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.10.0195439
MA0074.10.902074
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.339729
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.10.231323
MA0093.10.444403
MA0095.10
MA0098.10
MA0100.10.879972
MA0101.11.72541
MA0103.10.157724
MA0105.10.385363
MA0106.10.425111
MA0107.11.45792
MA0108.20.50131
MA0109.10
MA0111.11.26116
MA0113.11.03368
MA0114.11.10492
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.580747
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.231431
MA0140.10.330266
MA0141.10.511953
MA0142.10.547747
MA0143.10.414534
MA0144.11.64479
MA0145.10.189432
MA0146.10.0343188
MA0147.10.349075
MA0148.10.747422
MA0149.10.204102
MA0062.20.046824
MA0035.21.5961
MA0039.20.218113
MA0138.20.469076
MA0002.20.0664561
MA0137.22.9583
MA0104.20.257564
MA0047.20.380343
MA0112.20.370361
MA0065.20.371748
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.283993
MA0155.10.22104
MA0156.10.490212
MA0157.11.28808
MA0158.10
MA0159.10.114033
MA0160.10.274172
MA0161.10
MA0162.10.0134677
MA0163.10.0112325
MA0164.10.357779
MA0080.20.467794
MA0018.20.366212
MA0099.20.463355
MA0079.20.00214241
MA0102.21.35579
MA0258.10.0900907
MA0259.10.331447
MA0442.10
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