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MCL coexpression mm9:367: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!6.88e-35!75;UBERON:0001017!1.01e-34!73;UBERON:0002346!3.51e-34!64;UBERON:0003075!3.51e-34!64;UBERON:0007284!3.51e-34!64;UBERON:0004121!4.13e-33!95;UBERON:0000924!4.13e-33!95;UBERON:0006601!4.13e-33!95;UBERON:0000073!1.11e-29!54;UBERON:0010371!1.10e-28!73;UBERON:0001049!2.40e-28!52;UBERON:0005068!2.40e-28!52;UBERON:0006241!2.40e-28!52;UBERON:0007135!2.40e-28!52;UBERON:0003056!1.77e-26!49;UBERON:0000955!4.37e-24!47;UBERON:0006238!4.37e-24!47;UBERON:0002616!3.20e-23!46;UBERON:0010314!4.02e-23!92;UBERON:0002020!3.29e-22!34;UBERON:0003080!7.64e-22!40;UBERON:0002780!4.78e-21!39;UBERON:0001890!4.78e-21!39;UBERON:0006240!4.78e-21!39;UBERON:0003528!7.19e-18!29;UBERON:0002791!7.19e-18!29;UBERON:0001893!7.19e-18!29;UBERON:0000956!5.96e-12!21;UBERON:0001869!5.96e-12!21;UBERON:0000203!5.96e-12!21;UBERON:0002619!4.28e-09!17;UBERON:0002021!1.47e-07!10;UBERON:0000411!1.47e-07!10;UBERON:0001950!1.47e-07!10;UBERON:0002420!3.01e-07!8;UBERON:0007245!3.01e-07!8;UBERON:0010009!3.01e-07!8;UBERON:0010011!3.01e-07!8;UBERON:0000454!3.01e-07!8;UBERON:0003076!5.83e-07!12;UBERON:0003057!5.83e-07!12
|ontology_enrichment_uberon=UBERON:0001016!6.88e-35!75;UBERON:0001017!1.01e-34!73;UBERON:0002346!3.51e-34!64;UBERON:0003075!3.51e-34!64;UBERON:0007284!3.51e-34!64;UBERON:0004121!4.13e-33!95;UBERON:0000924!4.13e-33!95;UBERON:0006601!4.13e-33!95;UBERON:0000073!1.11e-29!54;UBERON:0010371!1.10e-28!73;UBERON:0001049!2.40e-28!52;UBERON:0005068!2.40e-28!52;UBERON:0006241!2.40e-28!52;UBERON:0007135!2.40e-28!52;UBERON:0003056!1.77e-26!49;UBERON:0000955!4.37e-24!47;UBERON:0006238!4.37e-24!47;UBERON:0002616!3.20e-23!46;UBERON:0010314!4.02e-23!92;UBERON:0002020!3.29e-22!34;UBERON:0003080!7.64e-22!40;UBERON:0002780!4.78e-21!39;UBERON:0001890!4.78e-21!39;UBERON:0006240!4.78e-21!39;UBERON:0003528!7.19e-18!29;UBERON:0002791!7.19e-18!29;UBERON:0001893!7.19e-18!29;UBERON:0000956!5.96e-12!21;UBERON:0001869!5.96e-12!21;UBERON:0000203!5.96e-12!21;UBERON:0002619!4.28e-09!17;UBERON:0002021!1.47e-07!10;UBERON:0000411!1.47e-07!10;UBERON:0001950!1.47e-07!10;UBERON:0002420!3.01e-07!8;UBERON:0007245!3.01e-07!8;UBERON:0010009!3.01e-07!8;UBERON:0010011!3.01e-07!8;UBERON:0000454!3.01e-07!8;UBERON:0003076!5.83e-07!12;UBERON:0003057!5.83e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.403818,0.729509,0.364203,0.15483,0.0572171,0.164217,0.644497,0.475556,0.808878,1.64858,0.570169,0.218542,1.12096,0.23628,0.497341,0,0.38962,0.0539173,0.429762,0.794788,0.0932143,0.216191,0.664014,0.206855,0.117721,0.256873,0.0827016,0.527289,0.26816,0.284323,0.504259,0.476579,1.63399,0.348165,0.857292,0.409149,0.728083,0.21594,0.365025,1.71775,0.203766,0.512679,0.186867,0.232623,0.653801,0.452134,0.865599,0.553328,0.243974,0.0792869,0.374992,0.277452,0.266413,0.603398,0.619345,0.677917,0.0837141,0.209397,0.0753109,0.240064,0.459084,0.777251,0.543433,0.365621,0.2499,0.399544,0.745869,1.08074,0.455021,0.938231,2.27484,0.108881,1.79533,0.650163,0.896361,1.16897,0.0142585,0.314806,0.444191,0.0954455,0.266969,0.404291,0.283653,0.240882,0.545133,4.3992,2.18397,1.41663,0.874441,1.23935,0.811671,0.549603,0.487824,0.216228,3.0171,0.580811,0.100987,0.490297,0.324141,0.632387,0.413671,0.476334,0.58753,0.375488,0.374608,0.171895,0.42513,0.186164,2.87571,1.07708,0.124464,0.58915,0.318143,0.199544,0.818358,0.20155,1.40911,0.475893,0.390716,0.180519,0.655146,0.348339,0.258253,0.314081,0.869916,0.447391,1.22688,0.481866,0.744444,0.220019,1.40249,0.896011,0.716744,0.701605,0.838892,0.211231,0.133745,0.991009,0.792231,1.60311,1.2081,0.750296,0.267427,0.48577,0.369214,0.172491,0.326451,1.56378,0.135184,1.22075,0.497376,4.64774,0.60483,0.942446,0.699993,0.680035,0.278231,0.526055,0.40004,1.33692,0.801233,0.544365,0.447776,0.779273,0.366469,0.687124,1.57028,0.62125,0.85239
|tfbs_overrepresentation_for_novel_motifs=0.403818,0.729509,0.364203,0.15483,0.0572171,0.164217,0.644497,0.475556,0.808878,1.64858,0.570169,0.218542,1.12096,0.23628,0.497341,0,0.38962,0.0539173,0.429762,0.794788,0.0932143,0.216191,0.664014,0.206855,0.117721,0.256873,0.0827016,0.527289,0.26816,0.284323,0.504259,0.476579,1.63399,0.348165,0.857292,0.409149,0.728083,0.21594,0.365025,1.71775,0.203766,0.512679,0.186867,0.232623,0.653801,0.452134,0.865599,0.553328,0.243974,0.0792869,0.374992,0.277452,0.266413,0.603398,0.619345,0.677917,0.0837141,0.209397,0.0753109,0.240064,0.459084,0.777251,0.543433,0.365621,0.2499,0.399544,0.745869,1.08074,0.455021,0.938231,2.27484,0.108881,1.79533,0.650163,0.896361,1.16897,0.0142585,0.314806,0.444191,0.0954455,0.266969,0.404291,0.283653,0.240882,0.545133,4.3992,2.18397,1.41663,0.874441,1.23935,0.811671,0.549603,0.487824,0.216228,3.0171,0.580811,0.100987,0.490297,0.324141,0.632387,0.413671,0.476334,0.58753,0.375488,0.374608,0.171895,0.42513,0.186164,2.87571,1.07708,0.124464,0.58915,0.318143,0.199544,0.818358,0.20155,1.40911,0.475893,0.390716,0.180519,0.655146,0.348339,0.258253,0.314081,0.869916,0.447391,1.22688,0.481866,0.744444,0.220019,1.40249,0.896011,0.716744,0.701605,0.838892,0.211231,0.133745,0.991009,0.792231,1.60311,1.2081,0.750296,0.267427,0.48577,0.369214,0.172491,0.326451,1.56378,0.135184,1.22075,0.497376,4.64774,0.60483,0.942446,0.699993,0.680035,0.278231,0.526055,0.40004,1.33692,0.801233,0.544365,0.447776,0.779273,0.366469,0.687124,1.57028,0.62125,0.85239
|tfbs_overrepresentation_jaspar=MA0003.1;6.23476,MA0004.1;0.916865,MA0006.1;0.839827,MA0007.1;0.145624,MA0009.1;0.499857,MA0014.1;3.96803,MA0017.1;0.074682,MA0019.1;0.344318,MA0024.1;0.461433,MA0025.1;0.712532,MA0027.1;2.09948,MA0028.1;1.32193,MA0029.1;0.442582,MA0030.1;0.448261,MA0031.1;1.07215,MA0038.1;0.256813,MA0040.1;0.510947,MA0041.1;0.109446,MA0042.1;0.102161,MA0043.1;0.586618,MA0046.1;0.531807,MA0048.1;1.61436,MA0050.1;0.180744,MA0051.1;0.263603,MA0052.1;0.518112,MA0055.1;0.0713525,MA0056.1;0,MA0057.1;3.78755,MA0058.1;0.666793,MA0059.1;0.342591,MA0060.1;0.0321237,MA0061.1;0.372144,MA0063.1;0,MA0066.1;0.248543,MA0067.1;0.817149,MA0068.1;0.598233,MA0069.1;0.518414,MA0070.1;0.509795,MA0071.1;1.01954,MA0072.1;0.502282,MA0073.1;2.16193,MA0074.1;0.222108,MA0076.1;1.00481,MA0077.1;0.48317,MA0078.1;0.289095,MA0081.1;0.37696,MA0083.1;0.585897,MA0084.1;1.1333,MA0087.1;0.546952,MA0088.1;0.570438,MA0089.1;0,MA0090.1;0.133736,MA0091.1;0.163657,MA0092.1;0.133927,MA0093.1;0.906819,MA0095.1;0,MA0098.1;0,MA0100.1;0.213782,MA0101.1;0.110172,MA0103.1;0.273906,MA0105.1;1.57652,MA0106.1;0.295186,MA0107.1;0.265519,MA0108.2;0.363107,MA0109.1;0,MA0111.1;0.863236,MA0113.1;0.273246,MA0114.1;0.0414319,MA0115.1;0.589161,MA0116.1;2.33104,MA0117.1;0.559943,MA0119.1;0.722506,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;0.301299,MA0142.1;0.40532,MA0143.1;0.285913,MA0144.1;0.0425459,MA0145.1;0.416713,MA0146.1;0.312675,MA0147.1;1.54322,MA0148.1;2.18836,MA0149.1;0.113293,MA0062.2;1.62311,MA0035.2;0.217072,MA0039.2;5.05637,MA0138.2;1.59561,MA0002.2;0.10237,MA0137.2;0.0883456,MA0104.2;1.19869,MA0047.2;2.02703,MA0112.2;0.416692,MA0065.2;1.173,MA0150.1;0.87649,MA0151.1;0,MA0152.1;0.256315,MA0153.1;0.635107,MA0154.1;1.59128,MA0155.1;2.06649,MA0156.1;0.59518,MA0157.1;0.378326,MA0158.1;0,MA0159.1;0.190402,MA0160.1;0.167661,MA0161.1;0,MA0162.1;9.26693,MA0163.1;5.63653,MA0164.1;0.23692,MA0080.2;0.0773362,MA0018.2;0.244112,MA0099.2;0.329046,MA0079.2;17.6211,MA0102.2;1.18455,MA0258.1;0.145568,MA0259.1;0.0431217,MA0442.1;0
}}
}}

Revision as of 11:38, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:101888238..101888276,-p1@Mpp3
Mm9::chr12:99812895..99812929,-p2@Kcnk10
Mm9::chr14:64225328..64225364,+p2@Xkr6
Mm9::chr15:76350293..76350321,-p@chr15:76350293..76350321
-
Mm9::chr15:77786878..77786899,-p2@Foxred2
Mm9::chr19:4711345..4711354,+p17@Spnb3
Mm9::chr19:4712071..4712111,+p3@Spnb3
Mm9::chr1:133421988..133422005,-p14@Srgap2
Mm9::chr2:152857721..152857750,+p1@Xkr7
Mm9::chr2:155601069..155601128,+p1@Mmp24
Mm9::chr2:181501710..181501742,+p2@Myt1
Mm9::chr2:181501745..181501778,+p1@Myt1
Mm9::chr4:115894282..115894293,+p4@Pik3r3
Mm9::chr5:21850488..21850499,-p2@Reln
Mm9::chr5:21850513..21850528,-p1@Reln
Mm9::chr5:37671788..37671812,+p@chr5:37671788..37671812
+
Mm9::chr5:37680151..37680172,+p@chr5:37680151..37680172
+
Mm9::chr7:51591045..51591057,+p7@Shank1
Mm9::chr9:108728357..108728405,+p1@Celsr3
Mm9::chr9:29220220..29220263,-p2@Ntm
Mm9::chr9:34296306..34296330,+p1@Kirrel3


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

no results for this coexpression

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
nervous system6.88e-3575
central nervous system1.01e-3473
neurectoderm3.51e-3464
neural plate3.51e-3464
presumptive neural plate3.51e-3464
ectoderm-derived structure4.13e-3395
ectoderm4.13e-3395
presumptive ectoderm4.13e-3395
regional part of nervous system1.11e-2954
ecto-epithelium1.10e-2873
neural tube2.40e-2852
neural rod2.40e-2852
future spinal cord2.40e-2852
neural keel2.40e-2852
pre-chordal neural plate1.77e-2649
brain4.37e-2447
future brain4.37e-2447
regional part of brain3.20e-2346
structure with developmental contribution from neural crest4.02e-2392
gray matter3.29e-2234
anterior neural tube7.64e-2240
regional part of forebrain4.78e-2139
forebrain4.78e-2139
future forebrain4.78e-2139
brain grey matter7.19e-1829
regional part of telencephalon7.19e-1829
telencephalon7.19e-1829
cerebral cortex5.96e-1221
cerebral hemisphere5.96e-1221
pallium5.96e-1221
regional part of cerebral cortex4.28e-0917
occipital lobe1.47e-0710
visual cortex1.47e-0710
neocortex1.47e-0710
basal ganglion3.01e-078
nuclear complex of neuraxis3.01e-078
aggregate regional part of brain3.01e-078
collection of basal ganglia3.01e-078
cerebral subcortex3.01e-078
posterior neural tube5.83e-0712
chordal neural plate5.83e-0712


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)
MA0003.16.23476
MA0004.10.916865
MA0006.10.839827
MA0007.10.145624
MA0009.10.499857
MA0014.13.96803
MA0017.10.074682
MA0019.10.344318
MA0024.10.461433
MA0025.10.712532
MA0027.12.09948
MA0028.11.32193
MA0029.10.442582
MA0030.10.448261
MA0031.11.07215
MA0038.10.256813
MA0040.10.510947
MA0041.10.109446
MA0042.10.102161
MA0043.10.586618
MA0046.10.531807
MA0048.11.61436
MA0050.10.180744
MA0051.10.263603
MA0052.10.518112
MA0055.10.0713525
MA0056.10
MA0057.13.78755
MA0058.10.666793
MA0059.10.342591
MA0060.10.0321237
MA0061.10.372144
MA0063.10
MA0066.10.248543
MA0067.10.817149
MA0068.10.598233
MA0069.10.518414
MA0070.10.509795
MA0071.11.01954
MA0072.10.502282
MA0073.12.16193
MA0074.10.222108
MA0076.11.00481
MA0077.10.48317
MA0078.10.289095
MA0081.10.37696
MA0083.10.585897
MA0084.11.1333
MA0087.10.546952
MA0088.10.570438
MA0089.10
MA0090.10.133736
MA0091.10.163657
MA0092.10.133927
MA0093.10.906819
MA0095.10
MA0098.10
MA0100.10.213782
MA0101.10.110172
MA0103.10.273906
MA0105.11.57652
MA0106.10.295186
MA0107.10.265519
MA0108.20.363107
MA0109.10
MA0111.10.863236
MA0113.10.273246
MA0114.10.0414319
MA0115.10.589161
MA0116.12.33104
MA0117.10.559943
MA0119.10.722506
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
MA0141.10.301299
MA0142.10.40532
MA0143.10.285913
MA0144.10.0425459
MA0145.10.416713
MA0146.10.312675
MA0147.11.54322
MA0148.12.18836
MA0149.10.113293
MA0062.21.62311
MA0035.20.217072
MA0039.25.05637
MA0138.21.59561
MA0002.20.10237
MA0137.20.0883456
MA0104.21.19869
MA0047.22.02703
MA0112.20.416692
MA0065.21.173
MA0150.10.87649
MA0151.10
MA0152.10.256315
MA0153.10.635107
MA0154.11.59128
MA0155.12.06649
MA0156.10.59518
MA0157.10.378326
MA0158.10
MA0159.10.190402
MA0160.10.167661
MA0161.10
MA0162.19.26693
MA0163.15.63653
MA0164.10.23692
MA0080.20.0773362
MA0018.20.244112
MA0099.20.329046
MA0079.217.6211
MA0102.21.18455
MA0258.10.145568
MA0259.10.0431217
MA0442.10
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