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MCL coexpression mm9:370: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0001017!8.29e-25!73;UBERON:0001016!1.08e-23!75;UBERON:0002020!3.86e-21!34;UBERON:0002384!8.36e-19!46;UBERON:0003528!1.50e-17!29;UBERON:0002791!1.50e-17!29;UBERON:0001893!1.50e-17!29;UBERON:0004121!5.89e-16!95;UBERON:0000924!5.89e-16!95;UBERON:0006601!5.89e-16!95;UBERON:0000073!1.19e-14!54;UBERON:0000956!3.22e-14!21;UBERON:0001869!3.22e-14!21;UBERON:0000203!3.22e-14!21;UBERON:0002619!4.63e-13!17;UBERON:0001049!2.11e-12!52;UBERON:0005068!2.11e-12!52;UBERON:0006241!2.11e-12!52;UBERON:0007135!2.11e-12!52;UBERON:0002021!1.62e-11!10;UBERON:0000411!1.62e-11!10;UBERON:0001950!1.62e-11!10;UBERON:0002346!1.79e-11!64;UBERON:0003075!1.79e-11!64;UBERON:0007284!1.79e-11!64;UBERON:0002780!6.72e-11!39;UBERON:0001890!6.72e-11!39;UBERON:0006240!6.72e-11!39;UBERON:0003080!1.99e-10!40;UBERON:0002616!6.23e-10!46;UBERON:0000955!1.52e-09!47;UBERON:0006238!1.52e-09!47;UBERON:0002371!1.84e-09!16;UBERON:0010371!9.62e-09!73;UBERON:0002410!8.47e-08!9;UBERON:0003056!9.68e-08!49
|tfbs_overrepresentation_for_novel_motifs=0.403818,0.0750114,0.11338,0.469866,0.458154,0.493109,0.227275,0.475556,0.112313,0.0667304,0.195931,0.623949,0.103499,0.665571,0.497341,0,0.38962,0.19894,0.0898284,0.0868811,0.310483,0.0140665,0.235613,0.790844,0.117721,0.256873,0.0183849,0.178177,0.0778495,0.139286,0.168752,0.476579,0.196184,0.348165,0.0646774,0.109578,0.0492863,0.21594,0.365025,0.0314971,0.782097,0.172188,0.186867,1.30257,0.000948158,0.885707,0.323935,0.188927,0.387527,0.0792869,0.374992,0.277452,0.0463743,0.603398,0.619345,0.241579,0.59572,0.209397,0.0753109,0.240064,0.459084,0.284775,0.124057,0.365621,0.2499,0.399544,0.745869,1.08074,0.455021,0.938231,0.102831,0.108881,0.016171,0.650163,0.0150431,0.0128935,0.0671053,0.845129,0.444191,0.65245,0.110035,0.404291,0.774697,0.0973679,0.545133,0.000236268,0.0120029,0.284701,0.327889,1.23935,0.811671,0.549603,0.487824,0.216228,0.356264,0.318866,0.248387,0.490297,0.324141,0.00714671,0.413671,0.476334,0.58753,0.375488,0.374608,0.171895,0.42513,0.186164,0.0980442,0.0941582,0.124464,0.58915,0.0960466,0.199544,0.818358,0.20155,0.004331,0.157255,0.390716,0.180519,1.57662,1.64557,0.258253,1.52425,0.869916,0.447391,0.233251,0.481866,0.744444,0.220019,0.572132,0.896011,0.716744,0.701605,0.838892,0.0456113,1.33798,0.17313,0.792231,1.60311,1.2081,1.77422,0.267427,0.48577,0.966134,2.98357,0.326451,1.56378,0.420463,0.0579622,0.010571,0.0016498,0.60483,0.0356935,0.251095,0.680035,0.278231,0.526055,0.797218,0.133575,0.801233,0.544365,0.447776,0.123129,0.366469,0.687124,0.183595,0.62125,0.000441529
|tfbs_overrepresentation_jaspar=MA0003.1;1.00812e-05,MA0004.1;0.15514,MA0006.1;0.224339,MA0007.1;0.145624,MA0009.1;1.24915,MA0014.1;3.96127e-05,MA0017.1;0.935226,MA0019.1;0.344318,MA0024.1;0.461433,MA0025.1;0.712532,MA0027.1;2.09948,MA0028.1;0.067163,MA0029.1;2.93049,MA0030.1;0.448261,MA0031.1;0.417663,MA0038.1;0.713204,MA0040.1;0.510947,MA0041.1;0.717677,MA0042.1;0.684042,MA0043.1;0.586618,MA0046.1;0.531807,MA0048.1;0.038539,MA0050.1;0.533529,MA0051.1;0.263603,MA0052.1;0.518112,MA0055.1;0.00255547,MA0056.1;0,MA0057.1;0.00588043,MA0058.1;0.0984787,MA0059.1;0.342591,MA0060.1;1.73264,MA0061.1;0.0422754,MA0063.1;0,MA0066.1;0.248543,MA0067.1;0.817149,MA0068.1;0.00634922,MA0069.1;0.518414,MA0070.1;0.509795,MA0071.1;0.180178,MA0072.1;0.502282,MA0073.1;1.12814e-11,MA0074.1;0.222108,MA0076.1;0.0840393,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;0.0497133,MA0089.1;0,MA0090.1;0.133736,MA0091.1;0.491727,MA0092.1;0.417266,MA0093.1;0.248744,MA0095.1;0,MA0098.1;0,MA0100.1;0.213782,MA0101.1;0.110172,MA0103.1;0.0799057,MA0105.1;0.0133959,MA0106.1;0.295186,MA0107.1;0.0769078,MA0108.2;0.363107,MA0109.1;0,MA0111.1;0.14244,MA0113.1;0.273246,MA0114.1;0.0414319,MA0115.1;0.589161,MA0116.1;0.224075,MA0117.1;0.559943,MA0119.1;0.356648,MA0122.1;0.577888,MA0124.1;1.80835,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;0.0230855,MA0140.1;1.15189,MA0141.1;0.0898383,MA0142.1;1.04528,MA0143.1;0.285913,MA0144.1;0.373777,MA0145.1;0.00295235,MA0146.1;8.22358e-05,MA0147.1;0.400991,MA0148.1;0.165681,MA0149.1;0.113293,MA0062.2;0.0144279,MA0035.2;1.16493,MA0039.2;6.09268e-08,MA0138.2;0.334152,MA0002.2;0.10237,MA0137.2;0.618368,MA0104.2;0.279424,MA0047.2;0.256234,MA0112.2;0.00295203,MA0065.2;0.0584336,MA0150.1;0.446676,MA0151.1;0,MA0152.1;0.256315,MA0153.1;0.635107,MA0154.1;0.0372685,MA0155.1;0.0237983,MA0156.1;0.284174,MA0157.1;0.378326,MA0158.1;0,MA0159.1;0.051085,MA0160.1;0.167661,MA0161.1;0,MA0162.1;0.000145355,MA0163.1;0.000986949,MA0164.1;0.667063,MA0080.2;0.266721,MA0018.2;0.244112,MA0099.2;0.329046,MA0079.2;1.60561e-14,MA0102.2;1.18455,MA0258.1;0.0367249,MA0259.1;0.0431217,MA0442.1;0
}}

Latest revision as of 15:11, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:68834407..68834410,+p@chr11:68834407..68834410
+
Mm9::chr15:88731061..88731064,-p@chr15:88731061..88731064
-
Mm9::chr15:88849649..88849658,+p1@ENSMUST00000082547
Mm9::chr16:72264646..72264650,-p@chr16:72264646..72264650
-
Mm9::chr18:64714320..64714324,+p@chr18:64714320..64714324
+
Mm9::chr18:7346008..7346012,-p@chr18:7346008..7346012
-
Mm9::chr18:77245471..77245474,+p@chr18:77245471..77245474
+
Mm9::chr1:146456236..146456244,-p1@ENSMUST00000157471
Mm9::chr1:48519136..48519137,-p1@ENSMUST00000083009
Mm9::chr3:48758645..48758646,+p1@ENSMUST00000083084
Mm9::chr3:72925786..72925790,+p@chr3:72925786..72925790
+
Mm9::chr4:32085713..32085717,-p1@ENSMUST00000122491
Mm9::chr4:83173669..83173671,-p1@ENSMUST00000082672
Mm9::chr5:115940240..115940260,+p1@ENSMUST00000101833
Mm9::chr5:70310332..70310338,+p1@ENSMUST00000122630
Mm9::chr6:136366332..136366337,+p1@ENSMUST00000157784
Mm9::chr7:106628212..106628217,-p1@Snord15b
Mm9::chr8:126881132..126881144,+p1@ENSMUST00000082730
Mm9::chr9:118376179..118376183,-p1@ENSMUST00000122566
Mm9::chr9:35087109..35087113,+p@chr9:35087109..35087113
+
Mm9::chrX:106205182..106205187,-p1@ENSMUST00000104464


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>

Cell Type
Ontology termp-valuen
animal cell1.69e-46115
eukaryotic cell1.69e-46115
somatic cell1.10e-44118
somatic stem cell3.79e-4291
multi fate stem cell3.79e-4291
stem cell6.43e-4297
neural cell1.60e-2943
non-terminally differentiated cell2.89e-2949
ectodermal cell1.57e-2844
neurectodermal cell1.57e-2844
embryonic cell4.52e-2870
neuron1.71e-2533
neuronal stem cell1.71e-2533
neuroblast1.71e-2533
electrically signaling cell1.71e-2533
electrically responsive cell6.28e-2539
electrically active cell6.28e-2539
motile cell7.02e-2254
CNS neuron (sensu Vertebrata)7.98e-2023
neuroblast (sensu Vertebrata)7.98e-2023
connective tissue cell8.36e-1946
mesenchymal cell8.36e-1946
hematopoietic lineage restricted progenitor cell1.04e-1125
hematopoietic cell2.75e-1032
hematopoietic oligopotent progenitor cell2.75e-1032
hematopoietic stem cell2.75e-1032
angioblastic mesenchymal cell2.75e-1032
hematopoietic multipotent progenitor cell2.75e-1032
myeloid lineage restricted progenitor cell2.47e-0913
myeloid cell5.36e-0816
common myeloid progenitor5.89e-0819
autonomic neuron8.47e-089
oligodendrocyte precursor cell6.49e-078

Uber Anatomy
Ontology termp-valuen
central nervous system8.29e-2573
nervous system1.08e-2375
gray matter3.86e-2134
connective tissue8.36e-1946
brain grey matter1.50e-1729
regional part of telencephalon1.50e-1729
telencephalon1.50e-1729
ectoderm-derived structure5.89e-1695
ectoderm5.89e-1695
presumptive ectoderm5.89e-1695
regional part of nervous system1.19e-1454
cerebral cortex3.22e-1421
cerebral hemisphere3.22e-1421
pallium3.22e-1421
regional part of cerebral cortex4.63e-1317
neural tube2.11e-1252
neural rod2.11e-1252
future spinal cord2.11e-1252
neural keel2.11e-1252
occipital lobe1.62e-1110
visual cortex1.62e-1110
neocortex1.62e-1110
neurectoderm1.79e-1164
neural plate1.79e-1164
presumptive neural plate1.79e-1164
regional part of forebrain6.72e-1139
forebrain6.72e-1139
future forebrain6.72e-1139
anterior neural tube1.99e-1040
regional part of brain6.23e-1046
brain1.52e-0947
future brain1.52e-0947
bone marrow1.84e-0916
ecto-epithelium9.62e-0973
autonomic nervous system8.47e-089
pre-chordal neural plate9.68e-0849


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)
MA0003.11.00812e-05
MA0004.10.15514
MA0006.10.224339
MA0007.10.145624
MA0009.11.24915
MA0014.13.96127e-05
MA0017.10.935226
MA0019.10.344318
MA0024.10.461433
MA0025.10.712532
MA0027.12.09948
MA0028.10.067163
MA0029.12.93049
MA0030.10.448261
MA0031.10.417663
MA0038.10.713204
MA0040.10.510947
MA0041.10.717677
MA0042.10.684042
MA0043.10.586618
MA0046.10.531807
MA0048.10.038539
MA0050.10.533529
MA0051.10.263603
MA0052.10.518112
MA0055.10.00255547
MA0056.10
MA0057.10.00588043
MA0058.10.0984787
MA0059.10.342591
MA0060.11.73264
MA0061.10.0422754
MA0063.10
MA0066.10.248543
MA0067.10.817149
MA0068.10.00634922
MA0069.10.518414
MA0070.10.509795
MA0071.10.180178
MA0072.10.502282
MA0073.11.12814e-11
MA0074.10.222108
MA0076.10.0840393
MA0077.10.48317
MA0078.10.289095
MA0081.10.37696
MA0083.10.585897
MA0084.11.1333
MA0087.10.546952
MA0088.10.0497133
MA0089.10
MA0090.10.133736
MA0091.10.491727
MA0092.10.417266
MA0093.10.248744
MA0095.10
MA0098.10
MA0100.10.213782
MA0101.10.110172
MA0103.10.0799057
MA0105.10.0133959
MA0106.10.295186
MA0107.10.0769078
MA0108.20.363107
MA0109.10
MA0111.10.14244
MA0113.10.273246
MA0114.10.0414319
MA0115.10.589161
MA0116.10.224075
MA0117.10.559943
MA0119.10.356648
MA0122.10.577888
MA0124.11.80835
MA0125.10.697415
MA0130.10
MA0131.10.340612
MA0132.10
MA0133.10
MA0135.10.619844
MA0136.10.236653
MA0139.10.0230855
MA0140.11.15189
MA0141.10.0898383
MA0142.11.04528
MA0143.10.285913
MA0144.10.373777
MA0145.10.00295235
MA0146.18.22358e-05
MA0147.10.400991
MA0148.10.165681
MA0149.10.113293
MA0062.20.0144279
MA0035.21.16493
MA0039.26.09268e-08
MA0138.20.334152
MA0002.20.10237
MA0137.20.618368
MA0104.20.279424
MA0047.20.256234
MA0112.20.00295203
MA0065.20.0584336
MA0150.10.446676
MA0151.10
MA0152.10.256315
MA0153.10.635107
MA0154.10.0372685
MA0155.10.0237983
MA0156.10.284174
MA0157.10.378326
MA0158.10
MA0159.10.051085
MA0160.10.167661
MA0161.10
MA0162.10.000145355
MA0163.10.000986949
MA0164.10.667063
MA0080.20.266721
MA0018.20.244112
MA0099.20.329046
MA0079.21.60561e-14
MA0102.21.18455
MA0258.10.0367249
MA0259.10.0431217
MA0442.10
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