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{{MCL_coexpression_mm9
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Latest revision as of 14:57, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79516368..79516410,+p1@Gpx4
Mm9::chr11:120459955..120459992,+p2@Anapc11
Mm9::chr11:4886886..4886897,+p3@Ap1b1
Mm9::chr12:8928848..8928860,+p@chr12:8928848..8928860
+
Mm9::chr15:84818388..84818448,-p1@5031439G07Rik
Mm9::chr15:99223663..99223679,+p5@Tmbim6
Mm9::chr17:27076409..27076470,-p1@Cuta
Mm9::chr17:27702623..27702702,-p1@AI413582
Mm9::chr17:34784132..34784161,+p1@Atf6b
Mm9::chr19:5106967..5107023,-p1@Rab1b
Mm9::chr19:5729618..5729700,-p2@Fam89b
Mm9::chr1:174242509..174242568,+p1@Igsf8
Mm9::chr1:97210184..97210254,+p1@Fam174a
Mm9::chr1:97210255..97210281,+p2@Fam174a
Mm9::chr2:119114461..119114507,+p1@Vps18
Mm9::chr3:88981385..88981465,+p1@Scamp3
Mm9::chr4:117559884..117559895,-p2@Atp6v0b
Mm9::chr4:117559897..117559958,-p1@Atp6v0b
Mm9::chr4:125773910..125773952,+p2@Lsm10
Mm9::chr4:135528489..135528533,-p1@Lypla2
Mm9::chr4:44025533..44025566,+p1@Clta
Mm9::chr5:121835581..121835599,-p1@Trafd1
Mm9::chr5:138705170..138705216,-p2@BC037034
Mm9::chr5:138705241..138705288,-p1@BC037034
Mm9::chr7:109054424..109054506,+p1@2400001E08Rik
Mm9::chr7:134352086..134352157,-p2@Tbc1d10b
Mm9::chr7:17323785..17323825,+p1@Ap2s1
Mm9::chr7:52715209..52715251,-p1@Ftl1
Mm9::chr8:106772399..106772469,-p1@Tk2
Mm9::chr8:108089885..108089971,-p1@Atp6v0d1
Mm9::chr8:125135518..125135563,+p1@Trappc2l
Mm9::chr8:73030609..73030665,-p1@2810428I15Rik
Mm9::chr8:73132160..73132229,-p1@Ssbp4
Mm9::chr9:20449236..20449283,+p1@Ubl5


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:0030118clathrin coat0.00103007122298327
GO:0006810transport0.00103007122298327
GO:0030132clathrin coat of coated pit0.00103007122298327
GO:0051234establishment of localization0.00103007122298327
GO:0008565protein transporter activity0.00103007122298327
GO:0031090organelle membrane0.00103007122298327
GO:0030117membrane coat0.00108040588994423
GO:0048475coated membrane0.00108040588994423
GO:0046907intracellular transport0.00110542519164257
GO:0051179localization0.00140422280644445
GO:0015031protein transport0.00153093705585413
GO:0006886intracellular protein transport0.00161306751112645
GO:0045184establishment of protein localization0.00171093958241412
GO:0030125clathrin vesicle coat0.00213343846402819
GO:0008104protein localization0.00213343846402819
GO:0051649establishment of cellular localization0.00213343846402819
GO:0051641cellular localization0.00213343846402819
GO:0033036macromolecule localization0.00213343846402819
GO:0030665clathrin coated vesicle membrane0.00213343846402819
GO:0012505endomembrane system0.00441195157246126
GO:0008553hydrogen-exporting ATPase activity, phosphorylative mechanism0.00441195157246126
GO:0030119AP-type membrane coat adaptor complex0.00441195157246126
GO:0030120vesicle coat0.00441195157246126
GO:0030131clathrin adaptor complex0.00441195157246126
GO:0006461protein complex assembly0.00470957795315152
GO:0030662coated vesicle membrane0.00478895219045733
GO:0022892substrate-specific transporter activity0.00480224779721872
GO:0044431Golgi apparatus part0.00493250926918007
GO:0044446intracellular organelle part0.00537977021139587
GO:0044422organelle part0.00537977021139587
GO:0005905coated pit0.00537977021139587
GO:0015985energy coupled proton transport, down electrochemical gradient0.00537977021139587
GO:0015986ATP synthesis coupled proton transport0.00537977021139587
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.0066582076626911
GO:0006754ATP biosynthetic process0.0066582076626911
GO:0006753nucleoside phosphate metabolic process0.0066582076626911
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.00666359935002401
GO:0016469proton-transporting two-sector ATPase complex0.00666359935002401
GO:0030659cytoplasmic vesicle membrane0.00684869670245069
GO:0046034ATP metabolic process0.00733965127932895
GO:0016192vesicle-mediated transport0.00733965127932895
GO:0005683snRNP U70.00733965127932895
GO:0030128clathrin coat of endocytic vesicle0.00733965127932895
GO:0030669clathrin-coated endocytic vesicle membrane0.00733965127932895
GO:0047066phospholipid-hydroperoxide glutathione peroxidase activity0.00733965127932895
GO:0030122AP-2 adaptor complex0.00733965127932895
GO:0030666endocytic vesicle membrane0.00733965127932895
GO:0045334clathrin-coated endocytic vesicle0.00733965127932895
GO:0009201ribonucleoside triphosphate biosynthetic process0.00733965127932895
GO:0009145purine nucleoside triphosphate biosynthetic process0.00733965127932895
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.00733965127932895
GO:0019829cation-transporting ATPase activity0.00784930021274493
GO:0009142nucleoside triphosphate biosynthetic process0.00803046940300961
GO:0009205purine ribonucleoside triphosphate metabolic process0.0080621608790061
GO:0044433cytoplasmic vesicle part0.0080621608790061
GO:0009199ribonucleoside triphosphate metabolic process0.0082424065135637
GO:0006119oxidative phosphorylation0.00827727366333041
GO:0009144purine nucleoside triphosphate metabolic process0.00827727366333041
GO:0015992proton transport0.00878214655816941
GO:0006752group transfer coenzyme metabolic process0.00896171348440969
GO:0012506vesicle membrane0.00932030532341178
GO:0009141nucleoside triphosphate metabolic process0.00932030532341178
GO:0009152purine ribonucleotide biosynthetic process0.0094993236673797
GO:0006818hydrogen transport0.009678152953148
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0101896217294751
GO:0009260ribonucleotide biosynthetic process0.0103682295299337
GO:0008334histone mRNA metabolic process0.0104502479417977
GO:0006398histone mRNA 3'-end processing0.0104502479417977
GO:0009150purine ribonucleotide metabolic process0.0109027702625417
GO:0006164purine nucleotide biosynthetic process0.0110805182261044
GO:0000139Golgi membrane0.0122874565081795
GO:0016043cellular component organization and biogenesis0.0122937969140547
GO:0009259ribonucleotide metabolic process0.0122937969140547
GO:0006163purine nucleotide metabolic process0.0133460554113547
GO:0030136clathrin-coated vesicle0.0133460554113547
GO:0004797thymidine kinase activity0.0140176496158612
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0155181757503771
GO:0009108coenzyme biosynthetic process0.0160676712181081
GO:0031410cytoplasmic vesicle0.0167030811733568
GO:0030135coated vesicle0.0171744129955214
GO:0031982vesicle0.0174130932340225
GO:0015078hydrogen ion transmembrane transporter activity0.0182903938285974
GO:0065003macromolecular complex assembly0.0195806801547763
GO:0051188cofactor biosynthetic process0.0195806801547763
GO:0015077monovalent inorganic cation transmembrane transporter activity0.0195806801547763
GO:0019136deoxynucleoside kinase activity0.0203864894195307
GO:0017069snRNA binding0.0203864894195307
GO:0033176proton-transporting V-type ATPase complex0.023635378738937
GO:0007032endosome organization and biogenesis0.023635378738937
GO:0016471vacuolar proton-transporting V-type ATPase complex0.023635378738937
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.025666442978984
GO:0043492ATPase activity, coupled to movement of substances0.025666442978984
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0258180711699936
GO:0015030Cajal body0.0258370423680537
GO:0015991ATP hydrolysis coupled proton transport0.0258370423680537
GO:0030130clathrin coat of trans-Golgi network vesicle0.0258370423680537
GO:0022607cellular component assembly0.0268907328992126
GO:0009165nucleotide biosynthetic process0.0270004433233914
GO:0012510trans-Golgi network transport vesicle membrane0.0283314092552593
GO:0015988energy coupled proton transport, against electrochemical gradient0.0283314092552593
GO:0015399primary active transmembrane transporter activity0.0284489783883669
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0284489783883669
GO:0022890inorganic cation transmembrane transporter activity0.029453131230454
GO:0004602glutathione peroxidase activity0.030630183309856
GO:0010038response to metal ion0.0333731215676864
GO:0008199ferric iron binding0.0333731215676864
GO:0030532small nuclear ribonucleoprotein complex0.0353561526702033
GO:0030660Golgi-associated vesicle membrane0.0353561526702033
GO:0030658transport vesicle membrane0.0353561526702033
GO:0019206nucleoside kinase activity0.0353561526702033
GO:0030140trans-Golgi network transport vesicle0.0382019566560164
GO:0017111nucleoside-triphosphatase activity0.0383366047387109
GO:0006732coenzyme metabolic process0.0388458469411079
GO:0030139endocytic vesicle0.0399241084609958
GO:0010035response to inorganic substance0.0399241084609958
GO:0006812cation transport0.0399695485103797
GO:0005768endosome0.0402453259276258
GO:0016462pyrophosphatase activity0.0411696170722686
GO:0044444cytoplasmic part0.0411696170722686
GO:0031124mRNA 3'-end processing0.0411696170722686
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.0411696170722686
GO:0016817hydrolase activity, acting on acid anhydrides0.0411696170722686
GO:0009117nucleotide metabolic process0.0451322533584478
GO:0006888ER to Golgi vesicle-mediated transport0.0451322533584478
GO:0005774vacuolar membrane0.0451322533584478
GO:0016023cytoplasmic membrane-bound vesicle0.0468035196720562
GO:0051186cofactor metabolic process0.0468035196720562
GO:0031123RNA 3'-end processing0.0468035196720562
GO:0005773vacuole0.0480836459269845
GO:0030133transport vesicle0.0483825743086711
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0483825743086711
GO:0031988membrane-bound vesicle0.0483825743086711



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
non-terminally differentiated cell1.63e-2249
ectodermal cell3.67e-2044
neurectodermal cell3.67e-2044
neural cell4.03e-2043
electrically responsive cell1.58e-1639
electrically active cell1.58e-1639
somatic cell3.05e-16118
animal cell1.16e-14115
eukaryotic cell1.16e-14115
somatic stem cell2.03e-1491
multi fate stem cell2.03e-1491
neuron2.81e-1433
neuronal stem cell2.81e-1433
neuroblast2.81e-1433
electrically signaling cell2.81e-1433
embryonic cell4.31e-1470
stem cell1.36e-1297
CNS neuron (sensu Vertebrata)4.78e-1223
neuroblast (sensu Vertebrata)4.78e-1223
migratory neural crest cell7.19e-0710
neuron associated cell7.19e-0710
glial cell (sensu Vertebrata)7.19e-0710
neuron associated cell (sensu Vertebrata)7.19e-0710
glial cell7.19e-0710
glioblast7.19e-0710
glioblast (sensu Vertebrata)7.19e-0710

Uber Anatomy
Ontology termp-valuen
nervous system1.81e-3075
central nervous system1.38e-2973
ectoderm-derived structure1.89e-2395
ectoderm1.89e-2395
presumptive ectoderm1.89e-2395
regional part of nervous system2.70e-2154
neural tube5.42e-2052
neural rod5.42e-2052
future spinal cord5.42e-2052
neural keel5.42e-2052
neurectoderm1.10e-1764
neural plate1.10e-1764
presumptive neural plate1.10e-1764
brain4.20e-1747
future brain4.20e-1747
regional part of brain6.21e-1746
gray matter1.27e-1634
anterior neural tube1.46e-1440
ecto-epithelium1.65e-1473
regional part of forebrain3.53e-1439
forebrain3.53e-1439
future forebrain3.53e-1439
brain grey matter4.67e-1429
regional part of telencephalon4.67e-1429
telencephalon4.67e-1429
structure with developmental contribution from neural crest1.15e-1192
pre-chordal neural plate1.25e-1149
cerebral cortex2.92e-1021
cerebral hemisphere2.92e-1021
pallium2.92e-1021
regional part of cerebral cortex5.66e-0917


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)
MA0003.11.8759
MA0004.13.03297
MA0006.11.31921
MA0007.10.82717
MA0009.10.337492
MA0014.16.29301
MA0017.10.241082
MA0019.10.205515
MA0024.10.820639
MA0025.10.530879
MA0027.11.89129
MA0028.16.63563
MA0029.10.287662
MA0030.10.292547
MA0031.10.266391
MA0038.10.425709
MA0040.10.347276
MA0041.10.155958
MA0042.10.036061
MA0043.10.415031
MA0046.10.365786
MA0048.11.41666
MA0050.10.59417
MA0051.10.862788
MA0052.10.353618
MA0055.10.2045
MA0056.10
MA0057.10.400394
MA0058.14.08724
MA0059.10.620066
MA0060.15.56512
MA0061.10.466178
MA0063.10
MA0066.10.41007
MA0067.10.629308
MA0068.10.0146185
MA0069.10.353886
MA0070.10.346258
MA0071.10.0830235
MA0072.10.339628
MA0073.10.0120521
MA0074.10.360358
MA0076.18.06312
MA0077.10.32285
MA0078.10.161775
MA0081.10.688174
MA0083.10.414379
MA0084.10.934141
MA0087.10.379309
MA0088.12.55794
MA0089.10
MA0090.10.198563
MA0091.10.0722516
MA0092.10.439746
MA0093.15.36672
MA0095.10
MA0098.10
MA0100.10.701922
MA0101.10.646174
MA0103.10.258738
MA0105.10.92278
MA0106.10.498719
MA0107.10.75593
MA0108.20.629361
MA0109.10
MA0111.10.467988
MA0113.10.149628
MA0114.10.0460994
MA0115.10.417336
MA0116.10.639448
MA0117.10.390961
MA0119.10.0405474
MA0122.10.407133
MA0124.10.581749
MA0125.10.516802
MA0130.10
MA0131.12.46035
MA0132.10
MA0133.10
MA0135.10.445266
MA0136.10.775995
MA0139.11.60281
MA0140.10.105959
MA0141.10.0297262
MA0142.10.255956
MA0143.10.159321
MA0144.10.468617
MA0145.12.04381
MA0146.13.5853
MA0147.10.509447
MA0148.10.0735508
MA0149.10.0420811
MA0062.25.79247
MA0035.20.108338
MA0039.24.91635
MA0138.20.197313
MA0002.20.0696121
MA0137.20.5305
MA0104.21.39556
MA0047.20.136816
MA0112.20.714902
MA0065.20.254159
MA0150.10.219664
MA0151.10
MA0152.10.424765
MA0153.10.459241
MA0154.10.448933
MA0155.11.34988
MA0156.10.807998
MA0157.10.233393
MA0158.10
MA0159.10.0603505
MA0160.10.0748272
MA0161.10
MA0162.14.44727
MA0163.10.427523
MA0164.10.122585
MA0080.20.47059
MA0018.20.800068
MA0099.20.193216
MA0079.21.71659
MA0102.20.984244
MA0258.10.415286
MA0259.10.727482
MA0442.10
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