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MCL coexpression mm9:1322: Difference between revisions

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{{MCL_coexpression_mm9
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regulation of axon extension;0.0383141410538382;16885!GO:0050772;positive regulation of axonogenesis;0.0383141410538382;16885!GO:0030516;regulation of axon extension;0.0383141410538382;16885!GO:0050769;positive regulation of neurogenesis;0.0383141410538382;16885!GO:0048675;axon extension;0.0383141410538382;16885!GO:0005925;focal adhesion;0.0383141410538382;16885!GO:0050770;regulation of axonogenesis;0.0383141410538382;16885!GO:0005924;cell-substrate adherens junction;0.0383141410538382;16885!GO:0048468;cell development;0.0383141410538382;217893,16885!GO:0030055;cell-matrix junction;0.0383141410538382;16885!GO:0050767;regulation of neurogenesis;0.0447704829281724;16885!GO:0046982;protein heterodimerization activity;0.049626476547434;16885!GO:0005912;adherens junction;0.049626476547434;16885!GO:0051094;positive regulation of developmental process;0.049626476547434;16885!GO:0016323;basolateral plasma membrane;0.049626476547434;16885!GO:0048869;cellular developmental process;0.049626476547434;217893,16885!GO:0030154;cell 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|gostat_on_MCL_coexpression=GO:0045773;positive regulation of axon extension;0.0383141410538382;16885!GO:0050772;positive regulation of axonogenesis;0.0383141410538382;16885!GO:0030516;regulation of axon extension;0.0383141410538382;16885!GO:0050769;positive regulation of neurogenesis;0.0383141410538382;16885!GO:0048675;axon extension;0.0383141410538382;16885!GO:0005925;focal adhesion;0.0383141410538382;16885!GO:0050770;regulation of axonogenesis;0.0383141410538382;16885!GO:0005924;cell-substrate adherens junction;0.0383141410538382;16885!GO:0048468;cell development;0.0383141410538382;217893,16885!GO:0030055;cell-matrix junction;0.0383141410538382;16885!GO:0050767;regulation of neurogenesis;0.0447704829281724;16885!GO:0046982;protein heterodimerization activity;0.049626476547434;16885!GO:0005912;adherens junction;0.049626476547434;16885!GO:0051094;positive regulation of developmental process;0.049626476547434;16885!GO:0016323;basolateral plasma membrane;0.049626476547434;16885!GO:0048869;cellular developmental process;0.049626476547434;217893,16885!GO:0030154;cell differentiation;0.049626476547434;217893,16885!
|ontology_enrichment_celltype=CL:0002319!6.57e-18!43;CL:0000221!8.51e-18!44;CL:0000133!8.51e-18!44;CL:0000540!1.31e-17!33;CL:0000047!1.31e-17!33;CL:0000031!1.31e-17!33;CL:0000404!1.31e-17!33;CL:0000117!3.24e-15!23;CL:0000337!3.24e-15!23;CL:0000055!5.37e-15!49;CL:0000393!3.94e-14!39;CL:0000211!3.94e-14!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!9.33e-32!75;UBERON:0001017!1.18e-31!73;UBERON:0004121!9.34e-29!95;UBERON:0000924!9.34e-29!95;UBERON:0006601!9.34e-29!95;UBERON:0002346!2.57e-26!64;UBERON:0003075!2.57e-26!64;UBERON:0007284!2.57e-26!64;UBERON:0000073!1.73e-24!54;UBERON:0001049!4.36e-23!52;UBERON:0005068!4.36e-23!52;UBERON:0006241!4.36e-23!52;UBERON:0007135!4.36e-23!52;UBERON:0010371!1.29e-22!73;UBERON:0010314!1.19e-19!92;UBERON:0000955!4.40e-19!47;UBERON:0006238!4.40e-19!47;UBERON:0002616!8.29e-19!46;UBERON:0003056!2.23e-18!49;UBERON:0002020!1.24e-17!34;UBERON:0003080!1.01e-16!40;UBERON:0002780!4.39e-16!39;UBERON:0001890!4.39e-16!39;UBERON:0006240!4.39e-16!39;UBERON:0003528!3.22e-14!29;UBERON:0002791!3.22e-14!29;UBERON:0001893!3.22e-14!29;UBERON:0000956!2.03e-09!21;UBERON:0001869!2.03e-09!21;UBERON:0000203!2.03e-09!21;UBERON:0000468!2.78e-08!333;UBERON:0002619!2.01e-07!17;UBERON:0000922!4.45e-07!320;UBERON:0003076!4.87e-07!12;UBERON:0003057!4.87e-07!12
|tfbs_overrepresentation_for_novel_motifs=2.1342,0.217198,0.464605,0.535892,0.346849,1.35778,1.55624,0.247459,0.257202,8.26573,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,1.3999,0.426133,1.17476,0.657163,0.345236,1.19059,0.686615,0.63639,0.572827,1.02135,0.181062,0.558142,0.960397,0.336199,0.204204,0.956447,0.0363535,3.28478,0.629145,0.820134,3.85348,0.342638,0.56353,0.0995018,0.366415,1.45501,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.995874,1.10437,1.12205,0.66551,0.406788,1.50238,0.21472,1.59383,2.16366,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,2.94103,0.253541,8.23368,1.156,5.09737,1.08629,0.204132,0.763395,0.922432,0.430551,0.254777,3.35681,0.722675,0.240896,2.36544,5.55221,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,2.2472,0.281222,0.244935,0.976308,0.775372,0.938145,1.56871,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,1.93262,1.47196,1.33732,0.340765,6.93501,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,1.63376,8.75335,1.10596,0.783181,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,3.3831
}}

Latest revision as of 16:44, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:114252596..114252681,+p1@Pacs2
Mm9::chr4:119165168..119165223,-p1@Rimkla
Mm9::chr5:135164426..135164433,-p5@Limk1
Mm9::chr5:135164438..135164457,-p2@Limk1
Mm9::chr5:135164465..135164507,-p1@Limk1
Mm9::chr5:135164509..135164520,-p4@Limk1


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:0045773positive regulation of axon extension0.0383141410538382
GO:0050772positive regulation of axonogenesis0.0383141410538382
GO:0030516regulation of axon extension0.0383141410538382
GO:0050769positive regulation of neurogenesis0.0383141410538382
GO:0048675axon extension0.0383141410538382
GO:0005925focal adhesion0.0383141410538382
GO:0050770regulation of axonogenesis0.0383141410538382
GO:0005924cell-substrate adherens junction0.0383141410538382
GO:0048468cell development0.0383141410538382
GO:0030055cell-matrix junction0.0383141410538382
GO:0050767regulation of neurogenesis0.0447704829281724
GO:0046982protein heterodimerization activity0.049626476547434
GO:0005912adherens junction0.049626476547434
GO:0051094positive regulation of developmental process0.049626476547434
GO:0016323basolateral plasma membrane0.049626476547434
GO:0048869cellular developmental process0.049626476547434
GO:0030154cell differentiation0.049626476547434



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 system9.33e-3275
central nervous system1.18e-3173
ectoderm-derived structure9.34e-2995
ectoderm9.34e-2995
presumptive ectoderm9.34e-2995
neurectoderm2.57e-2664
neural plate2.57e-2664
presumptive neural plate2.57e-2664
regional part of nervous system1.73e-2454
neural tube4.36e-2352
neural rod4.36e-2352
future spinal cord4.36e-2352
neural keel4.36e-2352
ecto-epithelium1.29e-2273
structure with developmental contribution from neural crest1.19e-1992
brain4.40e-1947
future brain4.40e-1947
regional part of brain8.29e-1946
pre-chordal neural plate2.23e-1849
gray matter1.24e-1734
anterior neural tube1.01e-1640
regional part of forebrain4.39e-1639
forebrain4.39e-1639
future forebrain4.39e-1639
brain grey matter3.22e-1429
regional part of telencephalon3.22e-1429
telencephalon3.22e-1429
cerebral cortex2.03e-0921
cerebral hemisphere2.03e-0921
pallium2.03e-0921
multi-cellular organism2.78e-08333
regional part of cerebral cortex2.01e-0717
embryo4.45e-07320
posterior neural tube4.87e-0712
chordal neural plate4.87e-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)
MA0003.15.57281
MA0004.10.536396
MA0006.10.359699
MA0007.11.29371
MA0009.10.987341
MA0014.110.9915
MA0017.10.387481
MA0019.11.87871
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.13.66642
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.11.71525
MA0056.10
MA0057.11.43735
MA0058.10.436487
MA0059.10.449345
MA0060.12.96129
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.13.74054
MA0071.10.575909
MA0072.10.990133
MA0073.10.00140584
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.725434
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.57901
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.14.53037
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.12.45468
MA0146.14.28855
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.29.96847
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.822245
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.16.83422
MA0163.10.0423021
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.23.78002
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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