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MCL coexpression mm9:2554: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=}}
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0,0,0,0,0,0,0,0.946406008762049,0.794090392529058,0.787944889917365,1.10654544825447,0.747018196227403,1.1046089237167,0.97912424012869,0.0416219695316507,0.053384101688745,0,0.342042457850035,0.338597400867953,0.20783892899892,0.408279862095176,0.225838285223358,0.0335946298219363,0.0429701015824518,0.0298988291256234,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.060949742349986,0,0.124677146027627,0,0,0,0,0,0,0,0,0,0,0.0814738246146344,0.854513851959281,0.870147562250751,0,0,0,0.0266729310181638,0.06146830772433,0.118526159018222,0,0,0,0,0,0,0,0.0272812328911525,0.0838298710884077,0.0276339967099239,0.101794247119466,0.120542856770629,0.11975896664409,0.0264995447268593,0,0.168488134987372,0.198845534762996,0.218358051808061,0.0518239084624399,0.0477820105339592,0,0.16409053543596,0.207789592643862,0.147853052076205,0.421497439690608,0.378724277076057,0.213194248472311,0,0.0105464367459272,0,0.089870634893658,0,0,0,0,0.165054317473075,0,0,0,0.0190753472649188,0,0,0,0.0283696382889128,0,0,0.144585766190706,0.749345003196731,0.0576701149435126,0.0231592211867425,0,0,0.02032355265126,0.0160940015753934,0,0,0.0391023317126931,0,0.0217063266948359,0.0818430262945954,0.0572299897922243,0,0.989286579395711,1.02151953226414,0.0658679077392947,0.0990537226072171,0.114128092013267,0.0993535752696539,0.250949812996631,0.574808947172235,0.260094179220868,0.969150273537923,0.848392339350015,0.282495297950949,0.379086271904631,0.014039427912235,0.116974034526969,0.133589575306843,0.0984948585530179,0.0354164873527408,0.0547648704873513,0.0479365822274169,0.151699034337307,0.222167209570935,0.190410640949107,0.173453855787685,0.0936751348050256,0,0,0.0234630905383716,0,0.0995276257329737,0,0.0270896151765207,0,0,0,0.109911399899815,0,0,0,0,0,0,0,0,0,0,0,0.0112844458274858,0,0,0,0.64109251632922,0.0283586353054281,0,0,0,0,0,0.0265967023096741,0.029068513524998,0,0,0,0,0,0,0,0.0283276255534183,0.0262901170742449,0,0.015660687675573,0,0,0.0256623481908917,0.0196259340864308,0.0177532615418556,0,0,0,0,0,0,0,0,0,0.0328380773353307,0,0,0,0,0.045799574939574,0,0,0,0,0.154883890026017,0,0,0,0,0,0.0563706794313653,0.0258054912402382,0.0211905676183425,0.0530816920388087,0.0214179370325552,0.153145597545364,0.0660076969624586,0.052177717644017,0,0,0,0.0636187716843317,0.195546068358491,0.257266832164516,0,0.0325892178866794,0,0,0,0,0,0,0,0,0,1.23862978357559,0.0384288787618118,0,0,0.0442098583417606,0,0.0314648259551332,0.0382396321089427,0,0,0,0,0,0,0,0,0,0.04241575046071,0,0,0.0281130801321805,0.129334496017964,0.109566993441385,0.058082662966597,0.068845707371011,0.0305171655333305,0,0,0.0220945066996137,0.0216686375930551,0,0.0163248575732391,0,0.0740586442457873,0.272577321011358,0.131953892471193,0.0543244007135577,0.045614627090981,0.0249837052527249,0.134282325019269,0.287011568408111,0.111774754841602,0.172695949709909,0.143120868801708,0,0,0.0267936475703112,0.0283124632898976,0,0,0.0183146507189827,0.0221467740893117,0.0336584528774773,0.0333683477944273,0.069957971098037,0,0.0201717422827811,0.0413836553923013,0.0732800426438812,0.0175851390538142,0.0225994036878694,0.0668394709942333,0.0354379919290707,0.0507054124051707,0,0,0.31879849245117,0.0534442774038548,0.204131921631766,0.29577880821375,0.194225326633985,0.100905549805607,0.22697320295507,0.239113010531361,0.166030019728838,0.166323914619548,0.219351714445686,0.299137568514674,0.283075755846479,0.279447413530815,0,0,0,0,0.0255698190552108,0.0249001161321988,0.0633929773739637,0.0281168167036011,0.058848730478439,1.02587187513676,0.99049033860924,1.01892323257591,1.01547453838585,0.99816487278701,1.05647473092015,0.868238867401598,0.928660319072044,1.03451643365758,0.971136662923027,0.0285902743717296,0,0.022819361633082,0,0.0782327207790035,0.0906578161971527,0.0290529610814799,0.0271199773786347,0.040292085331151,0.0326153702592452,0,0.0649194021759347,0.0358411799990137,0.047061147990806,0.0876762342828646,0,0.043192691758359,0.02553579847638,0.0870219126787703,0.106781836491689,0,0,0.0619157564037287,0,0.0379857155623515,0.0235169662252587,0,0.0338091069434337,0.0842582280955373,0.128961655631339,0.0324589403363489,0.0520649353182069,0,0.055260483794291,0.0255354818037453,0,0.0859922256434397,0,0.050677925439327,0.0288567708324674,0.0551542189060567|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.807750064546741,0.581582694899678,0.55324078965696,0.964658492161895,0.622305884652727,1.0453559630193,0.934779894480362,0,0.0800761525331175,0,0.289229082821354,0.3215809234774,0.266885070731364,0.225398799517185,0.202963684786284,0,0.0644551523736777,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0673620022139481,0.728530130822386,0.868396495596429,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.103807782330171,0,0.109123086691028,0.0866689030825281,0.135918568883708,0.0397493170902889,0,0,0.140841653605462,0.116346380288332,0.0538027986792206,0.0380188235580625,0,0.19266946376396,0.193893011938994,0.163875090269313,0.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Latest revision as of 18:43, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:3366142..3366151,+p5@Ipcef1
Mm9::chr10:3366185..3366194,+p3@Ipcef1
Mm9::chr10:3366220..3366244,+p2@Ipcef1


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
mature alpha-beta T cell1.27e-099
alpha-beta T cell1.27e-099
immature T cell1.27e-099
mature T cell1.27e-099
immature alpha-beta T cell1.27e-099
lymphoid lineage restricted progenitor cell4.18e-0912
T cell6.13e-0911
pro-T cell6.13e-0911
CD4-positive, alpha-beta T cell1.08e-088
lymphocyte4.27e-0813
common lymphoid progenitor4.27e-0813
thymocyte6.41e-076
double negative thymocyte6.41e-076
naive T cell6.41e-076
double-positive, alpha-beta thymocyte6.41e-076
CD4-positive, alpha-beta thymocyte6.41e-076
naive thymus-derived CD4-positive, alpha-beta T cell6.41e-076
DN4 thymocyte6.41e-076
DN1 thymic pro-T cell6.41e-076
DN2 thymocyte6.41e-076
DN3 thymocyte6.41e-076
immature single positive thymocyte6.41e-076
early T lineage precursor6.41e-076
mature CD4 single-positive thymocyte6.41e-076
resting double-positive thymocyte6.41e-076
double-positive blast6.41e-076
CD69-positive double-positive thymocyte6.41e-076
CD69-positive, CD4-positive single-positive thymocyte6.41e-076
CD4-positive, CD8-intermediate double-positive thymocyte6.41e-076
CD24-positive, CD4 single-positive thymocyte6.41e-076

Uber Anatomy
Ontology termp-valuen
neurectoderm2.01e-1664
neural plate2.01e-1664
presumptive neural plate2.01e-1664
neural tube8.24e-1552
neural rod8.24e-1552
future spinal cord8.24e-1552
neural keel8.24e-1552
regional part of nervous system1.32e-1454
gray matter1.18e-1334
organ part2.70e-1399
pre-chordal neural plate6.39e-1349
ecto-epithelium1.80e-1273
brain2.50e-1247
future brain2.50e-1247
hemopoietic organ5.15e-1229
immune organ5.15e-1229
craniocervical region6.27e-1236
thymus7.51e-1223
neck7.51e-1223
respiratory system epithelium7.51e-1223
hemolymphoid system gland7.51e-1223
pharyngeal epithelium7.51e-1223
thymic region7.51e-1223
pharyngeal gland7.51e-1223
entire pharyngeal arch endoderm7.51e-1223
thymus primordium7.51e-1223
early pharyngeal endoderm7.51e-1223
regional part of brain1.54e-1146
pharynx4.74e-1124
gland of gut4.74e-1124
upper respiratory tract4.74e-1124
chordate pharynx4.74e-1124
pharyngeal arch system4.74e-1124
pharyngeal region of foregut4.74e-1124
brain grey matter6.18e-1129
regional part of telencephalon6.18e-1129
telencephalon6.18e-1129
occipital lobe1.67e-1010
visual cortex1.67e-1010
neocortex1.67e-1010
organ segment2.31e-1035
anterior neural tube5.76e-1040
regional part of forebrain1.77e-0939
forebrain1.77e-0939
future forebrain1.77e-0939
anterior region of body2.80e-0943
central nervous system3.84e-0973
segment of respiratory tract4.93e-0927
regional part of cerebral cortex1.17e-0817
nervous system1.46e-0875
mixed endoderm/mesoderm-derived structure1.52e-0835
hemolymphoid system1.63e-0848
immune system1.63e-0848
cerebral cortex2.22e-0821
cerebral hemisphere2.22e-0821
pallium2.22e-0821
ectoderm-derived structure3.17e-0895
ectoderm3.17e-0895
presumptive ectoderm3.17e-0895
hematopoietic system4.82e-0845
blood island4.82e-0845
structure with developmental contribution from neural crest1.88e-0792


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)
MA0003.10.0699972
MA0004.10.801718
MA0006.10.60285
MA0007.11.84502
MA0009.11.27673
MA0014.10.133574
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.12.70765
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.932001
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.896032
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.11.62747
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.11.83298
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.21.06145
MA0035.20.903829
MA0039.20.0481552
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.11.65374
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.166764
MA0102.22.01714
MA0258.11.29343
MA0259.10.543506
MA0442.10
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