Personal tools

MCL coexpression mm9:218

From FANTOM5_SSTAR

Revision as of 11:22, 23 January 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Phase1 CAGE Peaks

 Short description
Mm9::chr11:4847994..4848012,-p1@Nefh
Mm9::chr11:55421321..55421324,-p14@Glra1
Mm9::chr11:55421419..55421506,-p1@Glra1
Mm9::chr11:55421691..55421706,-p6@Glra1
Mm9::chr11:55421712..55421719,-p10@Glra1
Mm9::chr11:55421783..55421797,-p7@Glra1
Mm9::chr11:55422049..55422061,-p4@Glra1
Mm9::chr11:55422065..55422098,-p3@Glra1
Mm9::chr11:55422099..55422115,-p5@Glra1
Mm9::chr11:55422124..55422129,-p9@Glra1
Mm9::chr11:55422131..55422165,-p2@Glra1
Mm9::chr11:55886412..55886420,+p@chr11:55886412..55886420
+
Mm9::chr12:114040857..114040876,-p1@Ahnak2
Mm9::chr13:100286621..100286632,-p3@Mtap1b
Mm9::chr14:121739423..121739435,-p@chr14:121739423..121739435
-
Mm9::chr14:34183323..34183333,-p1@ENSMUST00000137359
Mm9::chr14:48339462..48339479,+p@chr14:48339462..48339479
+
Mm9::chr16:58677946..58677957,+p@chr16:58677946..58677957
+
Mm9::chr17:26341262..26341275,+p@chr17:26341262..26341275
+
Mm9::chr17:43786636..43786644,-p10@Slc25a27
Mm9::chr17:54436510..54436520,-p@chr17:54436510..54436520
-
Mm9::chr17:69476739..69476749,+p@chr17:69476739..69476749
+
Mm9::chr17:69476754..69476785,+p@chr17:69476754..69476785
+
Mm9::chr19:17030450..17030470,+p4@Prune2
Mm9::chr2:101660614..101660617,-p@chr2:101660614..101660617
-
Mm9::chr2:112411598..112411619,+p@chr2:112411598..112411619
+
Mm9::chr2:31133553..31133564,+p@chr2:31133553..31133564
+
Mm9::chr3:94203194..94203255,+p2@Lingo4
Mm9::chr4:137176954..137176965,+p8@LOC674195
p8@Usp48
Mm9::chr5:118399577..118399601,+p@chr5:118399577..118399601
+
Mm9::chr5:5694559..5694581,-p5@Steap2
Mm9::chr6:126668903..126668952,+p@chr6:126668903..126668952
+
Mm9::chr6:20963159..20963195,-p1@ENSMUST00000157206
Mm9::chr7:51079819..51079830,+p4@Klk6
Mm9::chr7:51079863..51079887,+p3@Klk6
Mm9::chr7:51079889..51079927,+p1@Klk6
Mm9::chr7:51848386..51848395,+p@chr7:51848386..51848395
+
Mm9::chr7:57165677..57165684,+p10@Slc6a5
Mm9::chr7:57165685..57165707,+p1@Slc6a5
Mm9::chr7:57165722..57165728,+p9@Slc6a5


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:0005275amine transmembrane transporter activity0.0225085773427904
GO:0015370solute:sodium symporter activity0.0225085773427904
GO:0015294solute:cation symporter activity0.0225085773427904
GO:0015075ion transmembrane transporter activity0.0225085773427904
GO:0015837amine transport0.0225085773427904
GO:0008292acetylcholine biosynthetic process0.0225085773427904
GO:0042737drug catabolic process0.0225085773427904
GO:0005307choline:sodium symporter activity0.0225085773427904
GO:0042738exogenous drug catabolic process0.0225085773427904
GO:0050660FAD binding0.0225085773427904
GO:0000226microtubule cytoskeleton organization and biogenesis0.0225085773427904
GO:0006811ion transport0.0225085773427904
GO:0022891substrate-specific transmembrane transporter activity0.0225085773427904
GO:0044271nitrogen compound biosynthetic process0.0225085773427904
GO:0051926negative regulation of calcium ion transport0.0225085773427904
GO:0015871choline transport0.0225085773427904
GO:0043576regulation of respiratory gaseous exchange0.0225085773427904
GO:0060012synaptic transmission, glycinergic0.0225085773427904
GO:0008291acetylcholine metabolic process0.0225085773427904
GO:0015220choline transmembrane transporter activity0.0225085773427904
GO:0022857transmembrane transporter activity0.0225085773427904
GO:0006810transport0.0225085773427904
GO:0030001metal ion transport0.0225085773427904
GO:0051234establishment of localization0.0225085773427904
GO:0002087neurological control of breathing0.0225085773427904
GO:0004517nitric-oxide synthase activity0.0225085773427904
GO:0043267negative regulation of potassium ion transport0.0225085773427904
GO:0060081membrane hyperpolarization0.0225085773427904
GO:0045110intermediate filament bundle assembly0.0225085773427904
GO:0060080regulation of inhibitory postsynaptic membrane potential0.0225085773427904
GO:0015844monoamine transport0.0225085773427904
GO:0022892substrate-specific transporter activity0.0225707551282698
GO:0006814sodium ion transport0.0225707551282698
GO:0050662coenzyme binding0.0225707551282698
GO:0002028regulation of sodium ion transport0.0225707551282698
GO:0016594glycine binding0.0225707551282698
GO:0016934extracellular-glycine-gated chloride channel activity0.0225707551282698
GO:0043271negative regulation of ion transport0.0225707551282698
GO:0016933extracellular-glycine-gated ion channel activity0.0225707551282698
GO:0008504monoamine transmembrane transporter activity0.0225707551282698
GO:0042439ethanolamine and derivative metabolic process0.0225707551282698
GO:0005624membrane fraction0.0225707551282698
GO:0008324cation transmembrane transporter activity0.0225707551282698
GO:0006812cation transport0.0225707551282698
GO:0043266regulation of potassium ion transport0.0225707551282698
GO:0051346negative regulation of hydrolase activity0.0225707551282698
GO:0003016respiratory system process0.0225707551282698
GO:0060013righting reflex0.0225707551282698
GO:0006893Golgi to plasma membrane transport0.0225707551282698
GO:0017144drug metabolic process0.0225707551282698
GO:0015293symporter activity0.0225707551282698
GO:0015674di-, tri-valent inorganic cation transport0.0225707551282698
GO:0000267cell fraction0.0241222418234328
GO:0051179localization0.0241222418234328
GO:0050884neuromuscular process controlling posture0.0248976936058924
GO:0005883neurofilament0.0248976936058924
GO:0005519cytoskeletal regulatory protein binding0.0280372293627797
GO:0051924regulation of calcium ion transport0.0280372293627797
GO:0005886plasma membrane0.0299662575020012
GO:0048037cofactor binding0.0299662575020012
GO:0060004reflex0.0299662575020012
GO:0016597amino acid binding0.0299662575020012
GO:0045045secretory pathway0.0302828536927784
GO:0007017microtubule-based process0.0302828536927784
GO:0015291secondary active transmembrane transporter activity0.0302828536927784
GO:0001578microtubule bundle formation0.0302828536927784
GO:0060053neurofilament cytoskeleton0.0302828536927784
GO:0060052neurofilament cytoskeleton organization and biogenesis0.0302828536927784
GO:0045109intermediate filament organization0.0302828536927784
GO:0006892post-Golgi vesicle-mediated transport0.0322092060227591
GO:0007340acrosome reaction0.0322092060227591
GO:0010181FMN binding0.0322092060227591
GO:0007268synaptic transmission0.0322092060227591
GO:0050661NADP binding0.0344907557195294
GO:0032940secretion by cell0.03523425512745
GO:0048265response to pain0.03523425512745
GO:0043269regulation of ion transport0.03523425512745
GO:0001964startle response0.03523425512745
GO:0060078regulation of postsynaptic membrane potential0.03523425512745
GO:0007274neuromuscular synaptic transmission0.036319963501225
GO:0007271synaptic transmission, cholinergic0.036319963501225
GO:0004293tissue kallikrein activity0.036319963501225
GO:0042136neurotransmitter biosynthetic process0.036319963501225
GO:0019226transmission of nerve impulse0.0387874874124148
GO:0043176amine binding0.0408969489234937
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0447428136131082
GO:0006809nitric oxide biosynthetic process0.0447428136131082
GO:0046209nitric oxide metabolic process0.0447428136131082
GO:0051051negative regulation of transport0.0463080275310763
GO:0005328neurotransmitter:sodium symporter activity0.0463080275310763
GO:0046903secretion0.0468846965000058
GO:0007585respiratory gaseous exchange0.0478036782542486
GO:0017156calcium ion-dependent exocytosis0.0487159519888813
GO:0005326neurotransmitter transporter activity0.0487159519888813
GO:0045103intermediate filament-based process0.0487159519888813



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
posterior neural tube5.07e-2512
chordal neural plate5.07e-2512
regional part of nervous system4.02e-2254
central nervous system6.61e-1973
neural tube1.84e-1852
neural rod1.84e-1852
future spinal cord1.84e-1852
neural keel1.84e-1852
spinal cord1.95e-186
dorsal region element1.95e-186
dorsum1.95e-186
nervous system2.80e-1875
neurectoderm8.78e-1864
neural plate8.78e-1864
presumptive neural plate8.78e-1864
ectoderm-derived structure2.19e-1695
ectoderm2.19e-1695
presumptive ectoderm2.19e-1695
regional part of spinal cord3.28e-155
gray matter of spinal cord3.28e-155
ecto-epithelium4.64e-1573
regional part of midbrain1.69e-134
midbrain1.69e-134
presumptive midbrain1.69e-134
midbrain neural tube1.69e-134
structure with developmental contribution from neural crest4.65e-1192
raphe nuclei1.20e-103
reticular formation1.20e-103
brain1.39e-1047
future brain1.39e-1047
substantia nigra2.15e-103
telencephalic nucleus2.15e-103
midbrain nucleus2.15e-103
neural nucleus2.15e-103
nucleus of brain2.15e-103
ventral horn of spinal cord1.67e-093
regional part of brain2.59e-0946
gray matter5.16e-0934
segmental subdivision of hindbrain5.42e-096
segmental subdivision of nervous system5.42e-096
hindbrain5.42e-096
presumptive hindbrain5.42e-096
medulla oblongata5.09e-082
brainstem5.09e-082
myelencephalon5.09e-082
future myelencephalon5.09e-082
dorsal horn of spinal cord2.42e-072


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)
MA0003.10.109885
MA0004.10.0463278
MA0006.10.471673
MA0007.10.161303
MA0009.10.28789
MA0014.10.0744222
MA0017.10.331109
MA0019.10.165823
MA0024.10.256408
MA0025.10.472823
MA0027.11.82121
MA0028.10.145873
MA0029.10.241245
MA0030.10.245792
MA0031.10.221516
MA0038.10.105238
MA0040.10.805237
MA0041.10.0256044
MA0042.10.243023
MA0043.10.361422
MA0046.10.314603
MA0048.11.00909
MA0050.10.0596944
MA0051.10.354431
MA0052.10.303096
MA0055.10.206037
MA0056.10
MA0057.10.147954
MA0058.10.0213244
MA0059.10.0239063
MA0060.10.864705
MA0061.10.00471153
MA0063.10
MA0066.10.0999207
MA0067.10.568484
MA0068.12.39708
MA0069.10.303349
MA0070.10.29615
MA0071.10.0593865
MA0072.10.289901
MA0073.14.33418
MA0074.11.48852
MA0076.10.192105
MA0077.10.274126
MA0078.10.79512
MA0081.10.12094
MA0083.10.360799
MA0084.10.868194
MA0087.10.873394
MA0088.11.33682
MA0089.10
MA0090.10.333785
MA0091.10.740061
MA0092.10.14376
MA0093.10.0119855
MA0095.10
MA0098.10
MA0100.10.269978
MA0101.10.0258982
MA0103.10.180657
MA0105.10.00429974
MA0106.10.40952
MA0107.10.0138193
MA0108.20.531039
MA0109.10
MA0111.10.359123
MA0113.10.371139
MA0114.10.17479
MA0115.10.363622
MA0116.10.273529
MA0117.10.33849
MA0119.10.26679
MA0122.10.353887
MA0124.10.522168
MA0125.10.459209
MA0130.10
MA0131.10.163115
MA0132.10
MA0133.10
MA0135.10.390343
MA0136.10.308328
MA0139.10.0103686
MA0140.10.0784504
MA0141.10.40191
MA0142.10.211884
MA0143.10.124552
MA0144.12.16407
MA0145.10.318839
MA0146.10.0821475
MA0147.10.0315369
MA0148.10.192241
MA0149.10.274777
MA0062.20.018869
MA0035.20.0804587
MA0039.20.0152642
MA0138.22.8506
MA0002.20.486186
MA0137.21.33652
MA0104.20.013958
MA0047.20.341736
MA0112.20.0176922
MA0065.20.0784483
MA0150.11.02258
MA0151.10
MA0152.10.104915
MA0153.10.403751
MA0154.10.0491733
MA0155.10.730028
MA0156.10.0738285
MA0157.10.191171
MA0158.10
MA0159.10.389602
MA0160.10.195348
MA0161.10
MA0162.10.00102553
MA0163.10.146948
MA0164.11.57578
MA0080.20.173579
MA0018.20.320996
MA0099.20.915183
MA0079.20.597199
MA0102.20.917775
MA0258.10.00364251
MA0259.10.083201
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:218&oldid=2573613"