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MCL coexpression mm9:1502: Difference between revisions

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{{MCL_coexpression_mm9
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cell migration;0.0223494283522351;57778!GO:0005522;profilin binding;0.0223494283522351;57778!GO:0017048;Rho GTPase 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|ontology_enrichment_celltype=CL:0000791!1.87e-08!9;CL:0000789!1.87e-08!9;CL:0002420!1.87e-08!9;CL:0002419!1.87e-08!9;CL:0000790!1.87e-08!9;CL:0000838!5.98e-08!12;CL:0000624!1.62e-07!8;CL:0000084!2.97e-07!11;CL:0000827!2.97e-07!11;CL:0000542!4.87e-07!13;CL:0000051!4.87e-07!13
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.62e-13!54;UBERON:0002370!1.22e-12!23;UBERON:0000974!1.22e-12!23;UBERON:0004807!1.22e-12!23;UBERON:0005058!1.22e-12!23;UBERON:0003351!1.22e-12!23;UBERON:0009113!1.22e-12!23;UBERON:0003295!1.22e-12!23;UBERON:0009722!1.22e-12!23;UBERON:0005562!1.22e-12!23;UBERON:0007690!1.22e-12!23;UBERON:0001049!3.63e-12!52;UBERON:0005068!3.63e-12!52;UBERON:0006241!3.63e-12!52;UBERON:0007135!3.63e-12!52;UBERON:0006562!8.98e-12!24;UBERON:0003408!8.98e-12!24;UBERON:0001557!8.98e-12!24;UBERON:0001042!8.98e-12!24;UBERON:0008814!8.98e-12!24;UBERON:0009145!8.98e-12!24;UBERON:0000064!1.01e-11!99;UBERON:0004177!1.94e-11!29;UBERON:0005057!1.94e-11!29;UBERON:0002020!2.23e-10!34;UBERON:0000063!2.55e-10!35;UBERON:0000955!7.57e-10!47;UBERON:0006238!7.57e-10!47;UBERON:0001017!1.25e-09!73;UBERON:0000072!1.37e-09!27;UBERON:0002616!2.75e-09!46;UBERON:0001016!5.28e-09!75;UBERON:0000077!8.47e-09!35;UBERON:0002346!1.10e-08!64;UBERON:0003075!1.10e-08!64;UBERON:0007284!1.10e-08!64;UBERON:0002193!1.60e-08!48;UBERON:0002405!1.60e-08!48;UBERON:0003080!3.93e-08!40;UBERON:0002390!4.34e-08!45;UBERON:0003061!4.34e-08!45;UBERON:0003528!8.80e-08!29;UBERON:0002791!8.80e-08!29;UBERON:0001893!8.80e-08!29;UBERON:0002780!1.01e-07!39;UBERON:0001890!1.01e-07!39;UBERON:0006240!1.01e-07!39;UBERON:0002021!2.19e-07!10;UBERON:0000411!2.19e-07!10;UBERON:0001950!2.19e-07!10;UBERON:0010371!3.34e-07!73
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}}

Latest revision as of 17:02, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:13685980..13686007,+p6@Hivep2
Mm9::chr10:13686012..13686028,+p8@Hivep2
Mm9::chr10:13686045..13686050,+p17@Hivep2
Mm9::chr10:13686074..13686090,+p9@Hivep2
Mm9::chr11:103032160..103032175,+p7@Fmnl1


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:0006929substrate-bound cell migration0.0223494283522351
GO:0005522profilin binding0.0223494283522351
GO:0017048Rho GTPase binding0.0422028640333464



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
regional part of nervous system1.62e-1354
thymus1.22e-1223
neck1.22e-1223
respiratory system epithelium1.22e-1223
hemolymphoid system gland1.22e-1223
pharyngeal epithelium1.22e-1223
thymic region1.22e-1223
pharyngeal gland1.22e-1223
entire pharyngeal arch endoderm1.22e-1223
thymus primordium1.22e-1223
early pharyngeal endoderm1.22e-1223
neural tube3.63e-1252
neural rod3.63e-1252
future spinal cord3.63e-1252
neural keel3.63e-1252
pharynx8.98e-1224
gland of gut8.98e-1224
upper respiratory tract8.98e-1224
chordate pharynx8.98e-1224
pharyngeal arch system8.98e-1224
pharyngeal region of foregut8.98e-1224
organ part1.01e-1199
hemopoietic organ1.94e-1129
immune organ1.94e-1129
gray matter2.23e-1034
organ segment2.55e-1035
brain7.57e-1047
future brain7.57e-1047
central nervous system1.25e-0973
segment of respiratory tract1.37e-0927
regional part of brain2.75e-0946
nervous system5.28e-0975
mixed endoderm/mesoderm-derived structure8.47e-0935
neurectoderm1.10e-0864
neural plate1.10e-0864
presumptive neural plate1.10e-0864
hemolymphoid system1.60e-0848
immune system1.60e-0848
anterior neural tube3.93e-0840
hematopoietic system4.34e-0845
blood island4.34e-0845
brain grey matter8.80e-0829
regional part of telencephalon8.80e-0829
telencephalon8.80e-0829
regional part of forebrain1.01e-0739
forebrain1.01e-0739
future forebrain1.01e-0739
occipital lobe2.19e-0710
visual cortex2.19e-0710
neocortex2.19e-0710
ecto-epithelium3.34e-0773


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)
MA0003.14.54162
MA0004.10.603793
MA0006.10.419915
MA0007.11.43525
MA0009.11.06266
MA0014.10.418772
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.12.23359
MA0042.12.18647
MA0043.11.1618
MA0046.11.09955
MA0048.12.48306
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.11.06992
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.14.54943
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.11.08757
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.16.2889
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.13.29666
MA0103.11.16573
MA0105.18.81041
MA0106.10.809991
MA0107.14.0529
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.13.85075
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.12.01917
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.12.22941
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.476962
MA0146.10.21827
MA0147.10.378658
MA0148.10.621195
MA0149.13.32334
MA0062.20.254018
MA0035.20.700704
MA0039.20.140205
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.477991
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.587595
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.11.01146
MA0160.10.624415
MA0161.10
MA0162.10.0699535
MA0163.12.98593
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.25.05279
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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