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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=0.

Latest revision as of 16:50, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:3884740..3884761,+p5@Nat15
Mm9::chr2:178149217..178149296,+p1@9030418K01Rik
Mm9::chr6:51473923..51473940,+p4@Snx10
Mm9::chr6:51473944..51473975,+p1@Snx10
Mm9::chr6:51473978..51473996,+p3@Snx10
Mm9::chr9:74919334..74919376,+p1@Myo5a


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:0042641actomyosin0.00639146828849399
GO:0031585regulation of inositol-1,4,5-triphosphate receptor activity0.00639146828849399
GO:0032252secretory granule localization0.00639146828849399
GO:0030050vesicle transport along actin filament0.00639146828849399
GO:0031987locomotion during locomotory behavior0.00639146828849399
GO:0051643ER localization0.00639146828849399
GO:0032402melanosome transport0.00684743893447205
GO:0051904pigment granule transport0.00684743893447205
GO:0032401establishment of melanosome localization0.00684743893447205
GO:0042759long-chain fatty acid biosynthetic process0.00684743893447205
GO:0051010microtubule plus-end binding0.00684743893447205
GO:0051905establishment of pigment granule localization0.00684743893447205
GO:0000146microfilament motor activity0.00684743893447205
GO:0032400melanosome localization0.00684743893447205
GO:0051875pigment granule localization0.00766892149341399
GO:0033059cellular pigmentation0.00912866790551806
GO:0042640anagen0.00912866790551806
GO:0042438melanin biosynthetic process0.00912866790551806
GO:0048770pigment granule0.00912866790551806
GO:0006582melanin metabolic process0.00912866790551806
GO:0042470melanosome0.00912866790551806
GO:0051650establishment of vesicle localization0.0095848386593006
GO:0051648vesicle localization0.0100012967142336
GO:0048820hair follicle maturation0.0103830061576734
GO:0001676long-chain fatty acid metabolic process0.0106486534370301
GO:0030048actin filament-based movement0.0106486534370301
GO:0001750photoreceptor outer segment0.0106486534370301
GO:0030318melanocyte differentiation0.0108610311850524
GO:0050931pigment cell differentiation0.0108610311850524
GO:0031513nonmotile primary cilium0.0108610311850524
GO:0051656establishment of organelle localization0.0129823520730131
GO:0030073insulin secretion0.0137736750069838
GO:0046148pigment biosynthetic process0.0138911611130087
GO:0042552myelination0.0138911611130087
GO:0051640organelle localization0.0138911611130087
GO:0030072peptide hormone secretion0.0138911611130087
GO:0007272ensheathment of neurons0.0138911611130087
GO:0002790peptide secretion0.0138911611130087
GO:0048066pigmentation during development0.0138911611130087
GO:0008366axon ensheathment0.0138911611130087
GO:0042440pigment metabolic process0.0144862029615817
GO:0050885neuromuscular process controlling balance0.0145970639054319
GO:0001508regulation of action potential0.0155391195341524
GO:0042476odontogenesis0.0155391195341524
GO:0030141secretory granule0.0155391195341524
GO:0015833peptide transport0.0155391195341524
GO:0022404molting cycle process0.0155391195341524
GO:0001942hair follicle development0.0155391195341524
GO:0022405hair cycle process0.0155391195341524
GO:0046879hormone secretion0.0155391195341524
GO:0019748secondary metabolic process0.0155391195341524
GO:0042633hair cycle0.0155391195341524
GO:0042303molting cycle0.0155391195341524
GO:0050808synapse organization and biogenesis0.0156056127985497
GO:0008017microtubule binding0.0160174445644905
GO:0050905neuromuscular process0.0160729652707262
GO:0048589developmental growth0.0161265194510242
GO:0015631tubulin binding0.0181562253050883
GO:0016459myosin complex0.01818823858615
GO:0043025cell soma0.01818823858615
GO:0005929cilium0.0210229101406554
GO:0006633fatty acid biosynthetic process0.0213000895559757
GO:0046394carboxylic acid biosynthetic process0.02182826583531
GO:0016053organic acid biosynthetic process0.02182826583531
GO:0006887exocytosis0.0250172083399141
GO:0003001generation of a signal involved in cell-cell signaling0.0252164962971195
GO:0021700developmental maturation0.0259793518783454
GO:0008544epidermis development0.0270000399031442
GO:0030705cytoskeleton-dependent intracellular transport0.0270460255594416
GO:0043062extracellular structure organization and biogenesis0.0270460255594416
GO:0007398ectoderm development0.0272022899553399
GO:0005516calmodulin binding0.028413330086811
GO:0007601visual perception0.0286757235298887
GO:0050953sensory perception of light stimulus0.0286757235298887
GO:0005882intermediate filament0.0300718626747224
GO:0045111intermediate filament cytoskeleton0.0304281505131191
GO:0006810transport0.0347970781176703
GO:0051234establishment of localization0.0362315960432765
GO:0006631fatty acid metabolic process0.0386661471464807
GO:0035091phosphoinositide binding0.0388845594676022
GO:0030029actin filament-based process0.0388845594676022
GO:0045045secretory pathway0.040727047671163
GO:0016023cytoplasmic membrane-bound vesicle0.0421438815831945
GO:0051179localization0.0421438815831945
GO:0015629actin cytoskeleton0.0421438815831945
GO:0007268synaptic transmission0.0421438815831945
GO:0031988membrane-bound vesicle0.0425318253242861
GO:0005543phospholipid binding0.043280992698455
GO:0007626locomotory behavior0.043280992698455
GO:0032940secretion by cell0.0436428101117104
GO:0032787monocarboxylic acid metabolic process0.0446213235502635
GO:0019226transmission of nerve impulse0.046607445879055
GO:0008610lipid biosynthetic process0.0483457131246586
GO:0003779actin binding0.0490393355486805



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 system6.65e-1975
central nervous system8.94e-1973
ectoderm-derived structure1.15e-1695
ectoderm1.15e-1695
presumptive ectoderm1.15e-1695
neurectoderm1.59e-1664
neural plate1.59e-1664
presumptive neural plate1.59e-1664
structure with developmental contribution from neural crest1.86e-1592
regional part of nervous system2.23e-1554
neural tube3.27e-1452
neural rod3.27e-1452
future spinal cord3.27e-1452
neural keel3.27e-1452
gray matter1.73e-1334
ecto-epithelium8.78e-1373
pre-chordal neural plate2.29e-1249
brain4.46e-1247
future brain4.46e-1247
regional part of brain1.35e-1146
brain grey matter2.28e-1129
regional part of telencephalon2.28e-1129
telencephalon2.28e-1129
anterior neural tube3.93e-1140
regional part of forebrain1.27e-1039
forebrain1.27e-1039
future forebrain1.27e-1039
cerebral cortex7.49e-0821
cerebral hemisphere7.49e-0821
pallium7.49e-0821
occipital lobe1.45e-0710
visual cortex1.45e-0710
neocortex1.45e-0710
regional part of cerebral cortex4.04e-0717


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)
MA0003.16.22897
MA0004.10.536396
MA0006.11.68531
MA0007.11.29371
MA0009.10.987341
MA0014.13.9794
MA0017.10.387481
MA0019.10.800946
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
MA0042.11.12834
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.149949
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.113.2193
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.11.74419
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.11.16089
MA0103.10.398766
MA0105.10.199622
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
MA0139.10.682297
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.829535
MA0145.10.379391
MA0146.13.00399
MA0147.11.54778
MA0148.10.553294
MA0149.10.464445
MA0062.20.591842
MA0035.20.630778
MA0039.24.12392
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.21.33199
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.11.36931
MA0161.10
MA0162.11.08528
MA0163.11.95647
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.21.83891
MA0079.24.55588
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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