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MCL coexpression mm9:432: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0001016!2.79e-21!75;UBERON:0001017!1.13e-20!73;UBERON:0002384!1.06e-18!46;UBERON:0002020!3.99e-18!34;UBERON:0003528!1.27e-14!29;UBERON:0002791!1.27e-14!29;UBERON:0001893!1.27e-14!29;UBERON:0004121!1.05e-13!95;UBERON:0000924!1.05e-13!95;UBERON:0006601!1.05e-13!95;UBERON:0000073!2.54e-12!54;UBERON:0000956!6.11e-12!21;UBERON:0001869!6.11e-12!21;UBERON:0000203!6.11e-12!21;UBERON:0002619!3.82e-11!17;UBERON:0001049!3.79e-10!52;UBERON:0005068!3.79e-10!52;UBERON:0006241!3.79e-10!52;UBERON:0007135!3.79e-10!52;UBERON:0002021!5.56e-10!10;UBERON:0000411!5.56e-10!10;UBERON:0001950!5.56e-10!10;UBERON:0002346!5.12e-09!64;UBERON:0003075!5.12e-09!64;UBERON:0007284!5.12e-09!64;UBERON:0002371!5.36e-09!16;UBERON:0002780!1.07e-08!39;UBERON:0001890!1.07e-08!39;UBERON:0006240!1.07e-08!39;UBERON:0003080!2.78e-08!40;UBERON:0002616!7.17e-08!46;UBERON:0000955!1.58e-07!47;UBERON:0006238!1.58e-07!47
|tfbs_overrepresentation_for_novel_motifs=0.520555,0.00904452,0.157426,0.205657,0.0882392,0.216369,0.286882,0.165361,0.0467632,0.00312222,0.702345,0.277243,0.0430464,0.296787,0.322172,0,0.46143,0.596872,0.0373086,0.0589119,0.823639,0.0330286,0.802849,0.294623,0.16256,0.319311,0.13779,0.232181,0.114379,0.0925636,0.22152,0.552579,0.0827485,0.116244,0.0978183,0.0116846,0.0778621,0.274364,0.237064,0.0536011,0.290922,0.225414,0.182703,1.10854,0.00049788,0.573949,0.391673,0.244272,0.260796,0.116163,0.445973,0.341665,0.0860531,0.683824,0.700221,0.302599,0.385691,0.26711,0.127634,0.300938,0.534331,0.922742,0.192373,0.43605,0.311703,1.18928,0.829699,1.16897,0.530087,1.02503,0.144846,0.17272,0.0369163,0.731855,0.0291015,0.0256364,0.027847,0.381898,0.518764,0.422405,0.0458011,0.476893,1.64569,0.157538,0.623727,0.000989898,0.166857,0.0927017,0.395899,1.32869,0.896685,0.62835,0.564287,0.305814,0.0649512,0.207461,0.370414,0.56686,0.391893,0.073048,0.26831,0.552324,0.667487,1.13461,0.445567,0.225081,0.498793,0.676966,0.139088,0.134388,0.170493,1.60584,0.136675,0.256145,0.903482,0.085085,0.00200355,0.208431,0.462587,0.0759495,0.736964,1.07223,0.320815,0.381122,0.955823,0.522111,0.293459,0.558086,0.828246,0.310322,0.651613,0.580662,0.799981,0.313768,0.92434,0.00586127,0.181334,0.64263,0.876916,1.69384,1.29725,0.834212,0.330794,0.562149,0.439856,0.225756,1.02134,1.65442,0.539014,0.0892035,0.0217799,0.0270799,0.685297,0.215456,0.841089,0.762455,0.342508,0.104469,0.173692,0.181136,0.886073,0.622933,0.522515,0.50469,1.11397,0.827428,0.266569,0.757197,0.00211964
|tfbs_overrepresentation_jaspar=MA0003.1;0.000105157,MA0004.1;0.206012,MA0006.1;0.315449,MA0007.1;0.195085,MA0009.1;0.576798,MA0014.1;0.00199206,MA0017.1;0.722188,MA0019.1;1.06293,MA0024.1;0.536784,MA0025.1;0.795679,MA0027.1;2.19092,MA0028.1;0.100975,MA0029.1;0.51708,MA0030.1;0.523021,MA0031.1;0.490954,MA0038.1;0.319246,MA0040.1;0.588314,MA0041.1;2.79581,MA0042.1;3.46427,MA0043.1;0.666547,MA0046.1;0.609938,MA0048.1;0.0160841,MA0050.1;0.235075,MA0051.1;0.326637,MA0052.1;0.595747,MA0055.1;0.00123041,MA0056.1;0,MA0057.1;0.0134783,MA0058.1;0.139612,MA0059.1;0.147666,MA0060.1;1.1808,MA0061.1;0.518556,MA0063.1;0,MA0066.1;0.310219,MA0067.1;0.902253,MA0068.1;0.176958,MA0069.1;0.59606,MA0070.1;0.587119,MA0071.1;0.661266,MA0072.1;0.579318,MA0073.1;0.0689575,MA0074.1;0.281183,MA0076.1;0.122031,MA0077.1;0.559443,MA0078.1;0.354249,MA0081.1;0.490611,MA0083.1;0.665805,MA0084.1;1.22195,MA0087.1;0.625609,MA0088.1;0.101322,MA0089.1;0,MA0090.1;0.534933,MA0091.1;1.15975,MA0092.1;0.181545,MA0093.1;0.105788,MA0095.1;0,MA0098.1;0,MA0100.1;0.748039,MA0101.1;0.466845,MA0103.1;0.116929,MA0105.1;0.0264543,MA0106.1;0.360817,MA0107.1;0.113208,MA0108.2;0.433384,MA0109.1;0,MA0111.1;1.06448,MA0113.1;0.337108,MA0114.1;0.238352,MA0115.1;0.669167,MA0116.1;0.0949327,MA0117.1;0.639033,MA0119.1;0.154009,MA0122.1;0.657549,MA0124.1;1.98169,MA0125.1;0.780232,MA0130.1;0,MA0131.1;0.409473,MA0132.1;0,MA0133.1;0,MA0135.1;0.700734,MA0136.1;0.297196,MA0139.1;0.160584,MA0140.1;0.271883,MA0141.1;0.405018,MA0142.1;1.20233,MA0143.1;0.350815,MA0144.1;0.242681,MA0145.1;0.00768581,MA0146.1;0.000421045,MA0147.1;0.260161,MA0148.1;0.218033,MA0149.1;0.157322,MA0062.2;0.117092,MA0035.2;0.275617,MA0039.2;1.69513e-05,MA0138.2;0.402586,MA0002.2;0.164166,MA0137.2;0.127311,MA0104.2;0.1822,MA0047.2;0.318614,MA0112.2;0.0402239,MA0065.2;0.0404778,MA0150.1;0.567944,MA0151.1;0,MA0152.1;0.318703,MA0153.1;0.716409,MA0154.1;0.0155639,MA0155.1;0.138235,MA0156.1;0.121496,MA0157.1;0.4495,MA0158.1;0,MA0159.1;0.274824,MA0160.1;0.220282,MA0161.1;0,MA0162.1;0.00501935,MA0163.1;0.00400987,MA0164.1;0.297489,MA0080.2;0.365149,MA0018.2;0.305372,MA0099.2;1.02741,MA0079.2;1.38002e-05,MA0102.2;1.27355,MA0258.1;0.0609037,MA0259.1;0.244906,MA0442.1;0
}}

Latest revision as of 15:17, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:104477319..104477348,+p1@ENSMUST00000082498
Mm9::chr11:48596086..48596090,+p@chr11:48596086..48596090
+
Mm9::chr11:6525808..6525825,-p2@LOC100046166
p2@Tbrg4
Mm9::chr13:35754002..35754007,+p1@ENSMUST00000083244
Mm9::chr13:80297923..80297926,+p1@ENSMUST00000122712
Mm9::chr14:106660467..106660471,-p1@ENSMUST00000083259
Mm9::chr15:49812997..49812998,-p@chr15:49812997..49812998
-
Mm9::chr15:80870069..80870076,+p1@ENSMUST00000082653
Mm9::chr19:26334980..26334985,-p1@ENSMUST00000122640
Mm9::chr19:53205743..53205744,+p@chr19:53205743..53205744
+
Mm9::chr1:17257114..17257120,-p@chr1:17257114..17257120
-
Mm9::chr1:172958092..172958103,+p1@ENSMUST00000083971
Mm9::chr2:3208787..3208789,-p1@ENSMUST00000082795
Mm9::chr3:32910877..32910881,+p1@ENSMUST00000122716
Mm9::chr5:115939465..115939467,+p1@ENSMUST00000102044
Mm9::chr6:78861159..78861164,+p1@ENSMUST00000083352
Mm9::chr8:18500723..18500726,+p@chr8:18500723..18500726
+


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 cell3.31e-46115
eukaryotic cell3.31e-46115
somatic cell2.76e-44118
somatic stem cell6.90e-3991
multi fate stem cell6.90e-3991
stem cell1.26e-3897
neural cell2.14e-2843
embryonic cell2.97e-2870
non-terminally differentiated cell1.97e-2749
ectodermal cell2.16e-2744
neurectodermal cell2.16e-2744
motile cell1.20e-2354
neuron9.92e-2233
neuronal stem cell9.92e-2233
neuroblast9.92e-2233
electrically signaling cell9.92e-2233
electrically responsive cell9.93e-2139
electrically active cell9.93e-2139
connective tissue cell1.06e-1846
mesenchymal cell1.06e-1846
CNS neuron (sensu Vertebrata)1.61e-1723
neuroblast (sensu Vertebrata)1.61e-1723
hematopoietic lineage restricted progenitor cell5.20e-1525
myeloid lineage restricted progenitor cell2.70e-1113
hematopoietic cell7.52e-1132
hematopoietic oligopotent progenitor cell7.52e-1132
hematopoietic stem cell7.52e-1132
angioblastic mesenchymal cell7.52e-1132
hematopoietic multipotent progenitor cell7.52e-1132
myeloid cell1.92e-0916
leukocyte6.60e-0817
nongranular leukocyte6.60e-0817
megakaryocyte-erythroid progenitor cell8.59e-089
nucleate cell2.02e-0716
migratory neural crest cell2.37e-0710
neuron associated cell2.37e-0710
glial cell (sensu Vertebrata)2.37e-0710
neuron associated cell (sensu Vertebrata)2.37e-0710
glial cell2.37e-0710
glioblast2.37e-0710
glioblast (sensu Vertebrata)2.37e-0710
common myeloid progenitor3.13e-0719
oligodendrocyte precursor cell3.89e-078

Uber Anatomy
Ontology termp-valuen
nervous system2.79e-2175
central nervous system1.13e-2073
connective tissue1.06e-1846
gray matter3.99e-1834
brain grey matter1.27e-1429
regional part of telencephalon1.27e-1429
telencephalon1.27e-1429
ectoderm-derived structure1.05e-1395
ectoderm1.05e-1395
presumptive ectoderm1.05e-1395
regional part of nervous system2.54e-1254
cerebral cortex6.11e-1221
cerebral hemisphere6.11e-1221
pallium6.11e-1221
regional part of cerebral cortex3.82e-1117
neural tube3.79e-1052
neural rod3.79e-1052
future spinal cord3.79e-1052
neural keel3.79e-1052
occipital lobe5.56e-1010
visual cortex5.56e-1010
neocortex5.56e-1010
neurectoderm5.12e-0964
neural plate5.12e-0964
presumptive neural plate5.12e-0964
bone marrow5.36e-0916
regional part of forebrain1.07e-0839
forebrain1.07e-0839
future forebrain1.07e-0839
anterior neural tube2.78e-0840
regional part of brain7.17e-0846
brain1.58e-0747
future brain1.58e-0747


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)
MA0003.10.000105157
MA0004.10.206012
MA0006.10.315449
MA0007.10.195085
MA0009.10.576798
MA0014.10.00199206
MA0017.10.722188
MA0019.11.06293
MA0024.10.536784
MA0025.10.795679
MA0027.12.19092
MA0028.10.100975
MA0029.10.51708
MA0030.10.523021
MA0031.10.490954
MA0038.10.319246
MA0040.10.588314
MA0041.12.79581
MA0042.13.46427
MA0043.10.666547
MA0046.10.609938
MA0048.10.0160841
MA0050.10.235075
MA0051.10.326637
MA0052.10.595747
MA0055.10.00123041
MA0056.10
MA0057.10.0134783
MA0058.10.139612
MA0059.10.147666
MA0060.11.1808
MA0061.10.518556
MA0063.10
MA0066.10.310219
MA0067.10.902253
MA0068.10.176958
MA0069.10.59606
MA0070.10.587119
MA0071.10.661266
MA0072.10.579318
MA0073.10.0689575
MA0074.10.281183
MA0076.10.122031
MA0077.10.559443
MA0078.10.354249
MA0081.10.490611
MA0083.10.665805
MA0084.11.22195
MA0087.10.625609
MA0088.10.101322
MA0089.10
MA0090.10.534933
MA0091.11.15975
MA0092.10.181545
MA0093.10.105788
MA0095.10
MA0098.10
MA0100.10.748039
MA0101.10.466845
MA0103.10.116929
MA0105.10.0264543
MA0106.10.360817
MA0107.10.113208
MA0108.20.433384
MA0109.10
MA0111.11.06448
MA0113.10.337108
MA0114.10.238352
MA0115.10.669167
MA0116.10.0949327
MA0117.10.639033
MA0119.10.154009
MA0122.10.657549
MA0124.11.98169
MA0125.10.780232
MA0130.10
MA0131.10.409473
MA0132.10
MA0133.10
MA0135.10.700734
MA0136.10.297196
MA0139.10.160584
MA0140.10.271883
MA0141.10.405018
MA0142.11.20233
MA0143.10.350815
MA0144.10.242681
MA0145.10.00768581
MA0146.10.000421045
MA0147.10.260161
MA0148.10.218033
MA0149.10.157322
MA0062.20.117092
MA0035.20.275617
MA0039.21.69513e-05
MA0138.20.402586
MA0002.20.164166
MA0137.20.127311
MA0104.20.1822
MA0047.20.318614
MA0112.20.0402239
MA0065.20.0404778
MA0150.10.567944
MA0151.10
MA0152.10.318703
MA0153.10.716409
MA0154.10.0155639
MA0155.10.138235
MA0156.10.121496
MA0157.10.4495
MA0158.10
MA0159.10.274824
MA0160.10.220282
MA0161.10
MA0162.10.00501935
MA0163.10.00400987
MA0164.10.297489
MA0080.20.365149
MA0018.20.305372
MA0099.21.02741
MA0079.21.38002e-05
MA0102.21.27355
MA0258.10.0609037
MA0259.10.244906
MA0442.10
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