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MCL coexpression mm9:138: Difference between revisions

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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=0

Latest revision as of 14:45, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126680496..126680508,-p@chr10:126680496..126680508
-
Mm9::chr10:126680766..126680812,-p@chr10:126680766..126680812
-
Mm9::chr10:4518432..4518443,+p@chr10:4518432..4518443
+
Mm9::chr10:59592423..59592429,+p@chr10:59592423..59592429
+
Mm9::chr10:72136725..72136763,+p@chr10:72136725..72136763
+
Mm9::chr11:5889661..5889673,-p@chr11:5889661..5889673
-
Mm9::chr11:64816580..64816584,-p@chr11:64816580..64816584
-
Mm9::chr11:64845225..64845232,-p@chr11:64845225..64845232
-
Mm9::chr12:113032964..113032975,+p@chr12:113032964..113032975
+
Mm9::chr12:11393678..11393694,-p@chr12:11393678..11393694
-
Mm9::chr12:68223886..68223889,-p@chr12:68223886..68223889
-
Mm9::chr13:110851140..110851163,-p@chr13:110851140..110851163
-
Mm9::chr13:54864056..54864070,-p@chr13:54864056..54864070
-
Mm9::chr13:54864074..54864090,-p@chr13:54864074..54864090
-
Mm9::chr13:54864309..54864332,-p4@Sncb
Mm9::chr16:81624003..81624007,+p@chr16:81624003..81624007
+
Mm9::chr16:85080190..85080210,-p@chr16:85080190..85080210
-
Mm9::chr16:85103570..85103586,-p@chr16:85103570..85103586
-
Mm9::chr16:96715418..96715439,+p@chr16:96715418..96715439
+
Mm9::chr16:96746997..96747008,+p@chr16:96746997..96747008
+
Mm9::chr17:44175924..44175936,+p@chr17:44175924..44175936
+
Mm9::chr1:174204562..174204585,-p@chr1:174204562..174204585
-
Mm9::chr1:182002589..182002613,+p@chr1:182002589..182002613
+
Mm9::chr1:66460068..66460079,+p@chr1:66460068..66460079
+
Mm9::chr1:94972774..94972785,-p@chr1:94972774..94972785
-
Mm9::chr2:121126369..121126378,+p@chr2:121126369..121126378
+
Mm9::chr2:121126678..121126692,+p@chr2:121126678..121126692
+
Mm9::chr2:121129130..121129142,+p@chr2:121129130..121129142
+
Mm9::chr2:121129461..121129479,+p@chr2:121129461..121129479
+
Mm9::chr2:180844460..180844464,-p@chr2:180844460..180844464
-
Mm9::chr2:32193593..32193605,-p@chr2:32193593..32193605
-
Mm9::chr2:66109276..66109279,-p@chr2:66109276..66109279
-
Mm9::chr3:88566166..88566177,-p@chr3:88566166..88566177
-
Mm9::chr4:149021990..149022022,+p@chr4:149021990..149022022
+
Mm9::chr5:104518700..104518712,-p@chr5:104518700..104518712
-
Mm9::chr5:104521484..104521505,-p@chr5:104521484..104521505
-
Mm9::chr5:104521890..104521901,-p@chr5:104521890..104521901
-
Mm9::chr5:104521907..104521921,-p@chr5:104521907..104521921
-
Mm9::chr5:104521939..104521982,-p@chr5:104521939..104521982
-
Mm9::chr5:104521964..104522078,+p@chr5:104521964..104522078
+
Mm9::chr5:104522019..104522029,-p@chr5:104522019..104522029
-
Mm9::chr5:104522032..104522052,-p@chr5:104522032..104522052
-
Mm9::chr5:104522054..104522074,-p@chr5:104522054..104522074
-
Mm9::chr5:104522083..104522126,-p@chr5:104522083..104522126
-
Mm9::chr5:104522132..104522159,-p@chr5:104522132..104522159
-
Mm9::chr5:104522160..104522199,-p@chr5:104522160..104522199
-
Mm9::chr5:104522217..104522228,-p@chr5:104522217..104522228
-
Mm9::chr5:104522241..104522262,-p@chr5:104522241..104522262
-
Mm9::chr5:104522263..104522285,-p@chr5:104522263..104522285
-
Mm9::chr5:104522302..104522312,-p@chr5:104522302..104522312
-
Mm9::chr5:104522323..104522339,-p@chr5:104522323..104522339
-
Mm9::chr5:104522352..104522369,-p@chr5:104522352..104522369
-
Mm9::chr5:104522382..104522396,-p@chr5:104522382..104522396
-
Mm9::chr5:104523689..104523706,-p@chr5:104523689..104523706
-
Mm9::chr5:104523713..104523731,-p@chr5:104523713..104523731
-
Mm9::chr5:104526761..104526794,-p@chr5:104526761..104526794
-
Mm9::chr5:108954441..108954452,-p@chr5:108954441..108954452
-
Mm9::chr5:108954538..108954559,-p@chr5:108954538..108954559
-
Mm9::chr5:108977620..108977629,-p@chr5:108977620..108977629
-
Mm9::chr5:121391984..121391993,-p@chr5:121391984..121391993
-
Mm9::chr5:147284234..147284251,+p@chr5:147284234..147284251
+
Mm9::chr6:115194201..115194206,+p@chr6:115194201..115194206
+
Mm9::chr6:124710525..124710540,-p@chr6:124710525..124710540
-
Mm9::chr6:29349198..29349211,+p@chr6:29349198..29349211
+
Mm9::chr7:25774971..25774989,-p@chr7:25774971..25774989
-
Mm9::chr7:25784014..25784026,-p@chr7:25784014..25784026
-
Mm9::chr7:3655909..3655936,+p3@Rps9
Mm9::chr7:67122496..67122500,-p@chr7:67122496..67122500
-
Mm9::chr7:67122611..67122624,-p@chr7:67122611..67122624
-
Mm9::chr8:73279779..73279791,+p@chr8:73279779..73279791
+
Mm9::chr8:98238507..98238522,+p@chr8:98238507..98238522
+
Mm9::chr9:75021886..75021903,+p@chr9:75021886..75021903
+
Mm9::chrX:100381307..100381318,-p@chrX:100381307..100381318
-
Mm9::chrX:132335433..132335444,+p@chrX:132335433..132335444
+
Mm9::chrX:132335723..132335735,+p@chrX:132335723..132335735
+
Mm9::chrX:155910772..155910786,+p@chrX:155910772..155910786
+
Mm9::chrX:155910799..155910813,+p@chrX:155910799..155910813
+
Mm9::chrX:155920207..155920226,+p@chrX:155920207..155920226
+
Mm9::chrX:155920917..155920933,+p@chrX:155920917..155920933
+
Mm9::chrX:155927241..155927259,+p@chrX:155927241..155927259
+
Mm9::chrX:20272630..20272655,+p5@Cdk16
Mm9::chrX:7221265..7221279,+p2@Syp
Mm9::chrX:7229108..7229122,+p@chrX:7229108..7229122
+


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:0035235ionotropic glutamate receptor signaling pathway0.00111394947125536
GO:0007267cell-cell signaling0.00111394947125536
GO:0007268synaptic transmission0.00234198036627526
GO:0019226transmission of nerve impulse0.0027975133727282
GO:0007215glutamate signaling pathway0.0027975133727282
GO:0007632visual behavior0.0101992651112497
GO:0008542visual learning0.0101992651112497
GO:0007409axonogenesis0.0116576548436933
GO:0048667neuron morphogenesis during differentiation0.0116576548436933
GO:0048812neurite morphogenesis0.0116576548436933
GO:0010324membrane invagination0.0116576548436933
GO:0006897endocytosis0.0116576548436933
GO:0009628response to abiotic stimulus0.0116576548436933
GO:0000904cellular morphogenesis during differentiation0.0116576548436933
GO:0031175neurite development0.0116576548436933
GO:0008344adult locomotory behavior0.0116576548436933
GO:0048878chemical homeostasis0.0116576548436933
GO:0048666neuron development0.0116576548436933
GO:0044430cytoskeletal part0.0116576548436933
GO:0007612learning0.0116576548436933
GO:0040014regulation of multicellular organism growth0.0116576548436933
GO:0051428peptide hormone receptor binding0.0116576548436933
GO:0048790maintenance of presynaptic active zone structure0.0116576548436933
GO:0051602response to electrical stimulus0.0116576548436933
GO:0031629synaptic vesicle fusion to presynaptic membrane0.0116576548436933
GO:0051462regulation of cortisol secretion0.0116576548436933
GO:0031338regulation of vesicle fusion0.0116576548436933
GO:0051463negative regulation of cortisol secretion0.0116576548436933
GO:0031630regulation of synaptic vesicle fusion to presynaptic membrane0.0116576548436933
GO:0051233spindle midzone0.0116576548436933
GO:0043400cortisol secretion0.0116576548436933
GO:0060125negative regulation of growth hormone secretion0.0116576548436933
GO:0050975sensory perception of touch0.0116576548436933
GO:0048669collateral sprouting in the absence of injury0.0116576548436933
GO:0016044membrane organization and biogenesis0.0116576548436933
GO:0008021synaptic vesicle0.0116576548436933
GO:0006874cellular calcium ion homeostasis0.0138041655180267
GO:0055074calcium ion homeostasis0.0138041655180267
GO:0030534adult behavior0.0138041655180267
GO:0035264multicellular organism growth0.0138041655180267
GO:0006810transport0.0138041655180267
GO:0032990cell part morphogenesis0.0138041655180267
GO:0048858cell projection morphogenesis0.0138041655180267
GO:0030030cell projection organization and biogenesis0.0138041655180267
GO:0006875cellular metal ion homeostasis0.0138041655180267
GO:0051234establishment of localization0.0138041655180267
GO:0030182neuron differentiation0.0138041655180267
GO:0055065metal ion homeostasis0.0138041655180267
GO:0007611learning and/or memory0.0138041655180267
GO:0015630microtubule cytoskeleton0.0138041655180267
GO:0031410cytoplasmic vesicle0.0138041655180267
GO:0009416response to light stimulus0.0138041655180267
GO:0032469endoplasmic reticulum calcium ion homeostasis0.0138041655180267
GO:0016199axon midline choice point recognition0.0138041655180267
GO:0046825regulation of protein export from nucleus0.0138041655180267
GO:0051563smooth endoplasmic reticulum calcium ion homeostasis0.0138041655180267
GO:0051319G2 phase0.0138041655180267
GO:0000085G2 phase of mitotic cell cycle0.0138041655180267
GO:0030136clathrin-coated vesicle0.0138041655180267
GO:0031982vesicle0.0138460913315066
GO:0048699generation of neurons0.016113704388195
GO:0051049regulation of transport0.0168738222448918
GO:0042592homeostatic process0.0169071157587907
GO:0003001generation of a signal involved in cell-cell signaling0.017247822072276
GO:0030135coated vesicle0.017247822072276
GO:0001505regulation of neurotransmitter levels0.0173732855766031
GO:0022008neurogenesis0.0179311845349454
GO:0048668collateral sprouting0.0179325221783552
GO:0009314response to radiation0.0185274641007596
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0190430221587785
GO:0051179localization0.0191483259823631
GO:0050954sensory perception of mechanical stimulus0.0191483259823631
GO:0005737cytoplasm0.0191483259823631
GO:0055066di-, tri-valent inorganic cation homeostasis0.0191483259823631
GO:0030003cellular cation homeostasis0.0195814285200309
GO:0006906vesicle fusion0.0195814285200309
GO:0051124synaptic growth at neuromuscular junction0.0195814285200309
GO:0016198axon choice point recognition0.0195814285200309
GO:0060123regulation of growth hormone secretion0.0195814285200309
GO:0046676negative regulation of insulin secretion0.0195814285200309
GO:0016322neuron remodeling0.0195814285200309
GO:0004726non-membrane spanning protein tyrosine phosphatase activity0.0195814285200309
GO:0045931positive regulation of progression through mitotic cell cycle0.0195814285200309
GO:0055080cation homeostasis0.0200411252627956
GO:0016192vesicle-mediated transport0.022909331631087
GO:0003016respiratory system process0.0230772076637092
GO:0046887positive regulation of hormone secretion0.0230772076637092
GO:0016188synaptic vesicle maturation0.0230772076637092
GO:0005856cytoskeleton0.0243833862298391
GO:0030252growth hormone secretion0.0265545073997606
GO:0048011nerve growth factor receptor signaling pathway0.0265545073997606
GO:0043232intracellular non-membrane-bound organelle0.0265545073997606
GO:0043228non-membrane-bound organelle0.0265545073997606
GO:0003924GTPase activity0.0273138125323779
GO:0017111nucleoside-triphosphatase activity0.0273138125323779
GO:0005624membrane fraction0.0273138125323779
GO:0001967suckling behavior0.0288645494470792
GO:0032989cellular structure morphogenesis0.0288645494470792
GO:0000902cell morphogenesis0.0288645494470792
GO:0016462pyrophosphatase activity0.0295048682068776
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.0295048682068776
GO:0006873cellular ion homeostasis0.0295048682068776
GO:0055082cellular chemical homeostasis0.0295048682068776
GO:0016817hydrolase activity, acting on acid anhydrides0.0295048682068776
GO:0040008regulation of growth0.0295048682068776
GO:0006378mRNA polyadenylation0.0295048682068776
GO:0009755hormone-mediated signaling0.0295048682068776
GO:0046888negative regulation of hormone secretion0.0295048682068776
GO:0048488synaptic vesicle endocytosis0.0295048682068776
GO:0006878cellular copper ion homeostasis0.0295048682068776
GO:0044444cytoplasmic part0.0302245016017736
GO:0000267cell fraction0.031435029463894
GO:0035253ciliary rootlet0.0314640346506138
GO:0055070copper ion homeostasis0.0314640346506138
GO:0007617mating behavior0.0314640346506138
GO:0042551neuron maturation0.0314640346506138
GO:0050801ion homeostasis0.0335025643965554
GO:0005391sodium:potassium-exchanging ATPase activity0.0335025643965554
GO:0051047positive regulation of secretion0.0335025643965554
GO:0008088axon cargo transport0.0335025643965554
GO:0006611protein export from nucleus0.0335025643965554
GO:0051223regulation of protein transport0.0356598603309848
GO:0016079synaptic vesicle exocytosis0.0356598603309848
GO:0043631RNA polyadenylation0.0356598603309848
GO:0050796regulation of insulin secretion0.0356598603309848
GO:0000074regulation of progression through cell cycle0.0358862668556828
GO:0050877neurological system process0.0360720793774721
GO:0016050vesicle organization and biogenesis0.0362749626013154
GO:0046822regulation of nucleocytoplasmic transport0.0362749626013154
GO:0051048negative regulation of secretion0.0362749626013154
GO:0045787positive regulation of progression through cell cycle0.0362749626013154
GO:0051427hormone receptor binding0.0362749626013154
GO:0035265organ growth0.0362749626013154
GO:0008038neuron recognition0.0362749626013154
GO:0016023cytoplasmic membrane-bound vesicle0.0368193715543754
GO:0046907intracellular transport0.037543017046726
GO:0005874microtubule0.0375992703884459
GO:0031594neuromuscular junction0.0375992703884459
GO:0007274neuromuscular synaptic transmission0.0375992703884459
GO:0007618mating0.0375992703884459
GO:0031988membrane-bound vesicle0.0378230800137175
GO:0031124mRNA 3'-end processing0.0390802852374933
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0390802852374933
GO:0044441cilium part0.0390802852374933
GO:0019098reproductive behavior0.0390802852374933
GO:0007626locomotory behavior0.0394609606910202
GO:0022414reproductive process0.0406869366672434
GO:0065008regulation of biological quality0.0418663760645604
GO:0019725cellular homeostasis0.0420184018344276
GO:0003008system process0.0423956247907445
GO:0007399nervous system development0.0425041037872437
GO:0009725response to hormone stimulus0.0425736919022379
GO:0007613memory0.0443420510603472
GO:0000077DNA damage checkpoint0.0443420510603472
GO:0031123RNA 3'-end processing0.0443420510603472
GO:0007416synaptogenesis0.0463345616556885
GO:0017157regulation of exocytosis0.0463345616556885
GO:0006641triacylglycerol metabolic process0.0482750074580333
GO:0001725stress fiber0.0482750074580333
GO:0031570DNA integrity checkpoint0.0489492009198897
GO:0007528neuromuscular junction development0.0489492009198897
GO:0032432actin filament bundle0.0489492009198897
GO:0046883regulation of hormone secretion0.0489492009198897
GO:0007346regulation of progression through mitotic cell cycle0.0489492009198897
GO:0042417dopamine metabolic process0.0489492009198897



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 system1.27e-3854
neurectoderm9.41e-3664
neural plate9.41e-3664
presumptive neural plate9.41e-3664
neural tube1.36e-3552
neural rod1.36e-3552
future spinal cord1.36e-3552
neural keel1.36e-3552
central nervous system3.52e-3473
nervous system7.25e-3375
gray matter1.60e-3234
ecto-epithelium1.47e-2973
brain2.47e-2947
future brain2.47e-2947
ectoderm-derived structure5.50e-2995
ectoderm5.50e-2995
presumptive ectoderm5.50e-2995
regional part of brain3.16e-2846
pre-chordal neural plate2.05e-2649
brain grey matter2.82e-2629
regional part of telencephalon2.82e-2629
telencephalon2.82e-2629
anterior neural tube1.74e-2540
regional part of forebrain2.20e-2439
forebrain2.20e-2439
future forebrain2.20e-2439
structure with developmental contribution from neural crest1.49e-2292
cerebral cortex1.44e-1721
cerebral hemisphere1.44e-1721
pallium1.44e-1721
occipital lobe9.99e-1510
visual cortex9.99e-1510
neocortex9.99e-1510
regional part of cerebral cortex5.42e-1417
posterior neural tube3.10e-1012
chordal neural plate3.10e-1012
tube4.65e-10114
basal ganglion7.34e-108
nuclear complex of neuraxis7.34e-108
aggregate regional part of brain7.34e-108
collection of basal ganglia7.34e-108
cerebral subcortex7.34e-108
anatomical conduit1.22e-08122
spinal cord1.63e-086
dorsal region element1.63e-086
dorsum1.63e-086
regional part of spinal cord2.25e-075
gray matter of spinal cord2.25e-075


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)
MA0003.16.94311e-12
MA0004.10.0220952
MA0006.10.0471954
MA0007.10.136841
MA0009.10.109275
MA0014.11.03414e-09
MA0017.10.508864
MA0019.10.0421173
MA0024.10.0899821
MA0025.10.241615
MA0027.11.50773
MA0028.10.611804
MA0029.10.58293
MA0030.10.0837529
MA0031.10.0700796
MA0038.10.0183031
MA0040.10.368817
MA0041.10.607066
MA0042.11.61361
MA0043.10.15848
MA0046.10.398327
MA0048.13.4813e-05
MA0050.11.52135
MA0051.10.690467
MA0052.10.760902
MA0055.10.000166309
MA0056.10
MA0057.10.00232185
MA0058.10.0585027
MA0059.10.794682
MA0060.10.000839638
MA0061.10.0190577
MA0063.10
MA0066.10.938963
MA0067.10.319057
MA0068.10.00279809
MA0069.10.119167
MA0070.10.367208
MA0071.10.852277
MA0072.10.722709
MA0073.11.29337e-09
MA0074.10.527234
MA0076.10.0404451
MA0077.10.330629
MA0078.10.109295
MA0081.14.04522
MA0083.10.477845
MA0084.10.583888
MA0087.10.135069
MA0088.10.000227565
MA0089.10
MA0090.10.114576
MA0091.10.746763
MA0092.11.72879
MA0093.10.00904163
MA0095.10
MA0098.10
MA0100.10.0521274
MA0101.10.00820137
MA0103.10.0801774
MA0105.10.140484
MA0106.10.0274303
MA0107.10.367441
MA0108.20.0486077
MA0109.10
MA0111.10.24726
MA0113.10.0956638
MA0114.10.218283
MA0115.10.160031
MA0116.10.167359
MA0117.10.142573
MA0119.10.0298859
MA0122.10.908754
MA0124.10.768602
MA0125.10.231
MA0130.10
MA0131.10.0408933
MA0132.10
MA0133.10
MA0135.12.29011
MA0136.10.0673904
MA0139.10.408824
MA0140.10.756943
MA0141.10.187415
MA0142.10.858979
MA0143.13.08644
MA0144.10.0193532
MA0145.13.8076e-05
MA0146.16.43787e-07
MA0147.10.0027373
MA0148.10.323098
MA0149.10.0801168
MA0062.20.00332083
MA0035.20.7743
MA0039.23.18228e-15
MA0138.20.631145
MA0002.20.088712
MA0137.20.181869
MA0104.28.83929e-05
MA0047.20.402098
MA0112.20.0106814
MA0065.20.0197903
MA0150.10.0184717
MA0151.10
MA0152.10.208525
MA0153.10.553521
MA0154.10.178255
MA0155.10.178521
MA0156.10.0035132
MA0157.10.05421
MA0158.10
MA0159.10.19486
MA0160.10.329816
MA0161.10
MA0162.13.78714e-10
MA0163.17.58919e-05
MA0164.10.349738
MA0080.20.95554
MA0018.20.0157357
MA0099.20.963244
MA0079.20
MA0102.20.62983
MA0258.10.529854
MA0259.10.0199899
MA0442.10
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