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Coexpression cluster:C375: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.197853,0.065679,1.60143,1.2245,0.146421,0.368696,0.478966,0.497522,0.139834,0.404941,0.671758,0.545475,0.551712,0.15157,0.954725,0.680359,0.312612,0.0973406,0.386787,0.103823,0.0508801,0.51164,0.357972,0.0354608,0.519613,0.5812,0.284994,0.719641,0.973349,0.399407,0.298766,0.341173,0.188539,0.354273,0.818635,0.01456,0.270269,0.115713,0.713261,0.11725,0.11321,0.27793,0.431246,0.0361212,0.285955,0.224432,0.159157,1.59083,0.381848,0.973887,0.603841,0.16639,0.40926,1.04005,0.532737,0.466119,0.63584,0.417969,0.0543465,0.133632,0.976157,0.484178,1.06217,0.792735,0.171703,0.266103,0.611096,0.954146,0.33304,0.800453,0.554532,0.0114139,0.806218,0.530988,0.532069,0.160548,0.424496,1.39732,0.330507,0.0661366,0.10792,0.290785,0.171482,0.0541031,0.486416,0.522279,0.101368,0.11928,1.20635,1.04966,0.695939,0.463366,0.354445,0.387491,0.340966,0.422264,0.382031,0.388689,0.231068,0.0955711,0.232609,0.349965,0.384158,0.315425,0.25774,0.0972887,0.819287,0.456614,0.888211,1.73757,0.0549789,1.7624,0.411216,0.104282,0.652077,0.110297,0.851347,0.297213,0.264397,0.017641,0.523757,0.226179,0.113636,1.01317,0.753832,0.27955,0.154657,0.358416,0.561176,0.0884077,0.463953,0.30248,0.573914,0.176484,0.707783,0.354931,1.01975,0.11017,0.668879,1.49486,1.10037,0.634967,0.155698,0.385822,0.71827,0.807047,0.24704,1.33792,0.273743,0.19455,0.72532,0.0935083,0.464277,0.461256,0.160304,0.829202,1.16359,0.133083,0.0687147,0.208636,0.633868,0.448609,0.329893,0.212291,0.270734,0.170987,0.348084,0.157687,1.07542
|tfbs_overrepresentation_for_novel_motifs=0.197853,0.065679,1.60143,1.2245,0.146421,0.368696,0.478966,0.497522,0.139834,0.404941,0.671758,0.545475,0.551712,0.15157,0.954725,0.680359,0.312612,0.0973406,0.386787,0.103823,0.0508801,0.51164,0.357972,0.0354608,0.519613,0.5812,0.284994,0.719641,0.973349,0.399407,0.298766,0.341173,0.188539,0.354273,0.818635,0.01456,0.270269,0.115713,0.713261,0.11725,0.11321,0.27793,0.431246,0.0361212,0.285955,0.224432,0.159157,1.59083,0.381848,0.973887,0.603841,0.16639,0.40926,1.04005,0.532737,0.466119,0.63584,0.417969,0.0543465,0.133632,0.976157,0.484178,1.06217,0.792735,0.171703,0.266103,0.611096,0.954146,0.33304,0.800453,0.554532,0.0114139,0.806218,0.530988,0.532069,0.160548,0.424496,1.39732,0.330507,0.0661366,0.10792,0.290785,0.171482,0.0541031,0.486416,0.522279,0.101368,0.11928,1.20635,1.04966,0.695939,0.463366,0.354445,0.387491,0.340966,0.422264,0.382031,0.388689,0.231068,0.0955711,0.232609,0.349965,0.384158,0.315425,0.25774,0.0972887,0.819287,0.456614,0.888211,1.73757,0.0549789,1.7624,0.411216,0.104282,0.652077,0.110297,0.851347,0.297213,0.264397,0.017641,0.523757,0.226179,0.113636,1.01317,0.753832,0.27955,0.154657,0.358416,0.561176,0.0884077,0.463953,0.30248,0.573914,0.176484,0.707783,0.354931,1.01975,0.11017,0.668879,1.49486,1.10037,0.634967,0.155698,0.385822,0.71827,0.807047,0.24704,1.33792,0.273743,0.19455,0.72532,0.0935083,0.464277,0.461256,0.160304,0.829202,1.16359,0.133083,0.0687147,0.208636,0.633868,0.448609,0.329893,0.212291,0.270734,0.170987,0.348084,0.157687,1.07542
|tfbs_overrepresentation_jaspar=MA0003.1;2.92043,MA0004.1;0.68402,MA0006.1;0.14464,MA0007.1;0.639929,MA0009.1;0.429031,MA0014.1;0.500568,MA0017.1;0.185458,MA0019.1;0.188957,MA0024.1;0.9086,MA0025.1;0.544326,MA0027.1;1.97447,MA0028.1;0.160829,MA0029.1;0.358654,MA0030.1;0.349473,MA0031.1;0.809566,MA0038.1;0.483171,MA0040.1;0.363365,MA0041.1;0.111817,MA0042.1;0.65234,MA0043.1;0.429296,MA0046.1;0.419892,MA0048.1;1.12026,MA0050.1;0.654418,MA0051.1;0.476736,MA0052.1;1.70896,MA0055.1;1.07853,MA0056.1;0,MA0057.1;0.143357,MA0058.1;0.810579,MA0059.1;0.464811,MA0060.1;0.0102756,MA0061.1;0.620016,MA0063.1;0,MA0066.1;0.483822,MA0067.1;0.711124,MA0068.1;0.451179,MA0069.1;0.416668,MA0070.1;0.407339,MA0071.1;0.839953,MA0072.1;0.403605,MA0073.1;0.000275135,MA0074.1;1.48035,MA0076.1;0.065346,MA0077.1;0.397221,MA0078.1;0.633683,MA0081.1;0.212556,MA0083.1;1.11054,MA0084.1;0.887042,MA0087.1;0.401577,MA0088.1;0.42613,MA0089.1;0,MA0090.1;0.0714597,MA0091.1;0.3381,MA0092.1;0.0849313,MA0093.1;0.617114,MA0095.1;0,MA0098.1;0,MA0100.1;0.168841,MA0101.1;0.627154,MA0103.1;0.318372,MA0105.1;1.21636,MA0106.1;0.18641,MA0107.1;0.414244,MA0108.2;0.804276,MA0109.1;0,MA0111.1;0.955933,MA0113.1;0.573327,MA0114.1;0.65856,MA0115.1;0.640975,MA0116.1;0.423674,MA0117.1;1.16571,MA0119.1;1.15535,MA0122.1;0.483183,MA0124.1;0.60338,MA0125.1;0.528543,MA0130.1;0,MA0131.1;0.663587,MA0132.1;0,MA0133.1;0,MA0135.1;0.454747,MA0136.1;0.164568,MA0139.1;0.355529,MA0140.1;0.421202,MA0141.1;0.80074,MA0142.1;1.38281,MA0143.1;0.573609,MA0144.1;0.0711193,MA0145.1;0.685149,MA0146.1;1.57099,MA0147.1;1.03959,MA0148.1;0.743891,MA0149.1;0.129939,MA0062.2;0.00628534,MA0035.2;0.135068,MA0039.2;0.0326666,MA0138.2;1.85435,MA0002.2;0.124839,MA0137.2;0.167559,MA0104.2;0.745965,MA0047.2;0.528161,MA0112.2;1.07456,MA0065.2;0.516863,MA0150.1;0.24291,MA0151.1;0,MA0152.1;0.430874,MA0153.1;0.513757,MA0154.1;1.18887,MA0155.1;0.780312,MA0156.1;0.0444235,MA0157.1;0.708688,MA0158.1;0,MA0159.1;0.435001,MA0160.1;0.390619,MA0161.1;0,MA0162.1;0.0749742,MA0163.1;0.681668,MA0164.1;0.205602,MA0080.2;0.0373957,MA0018.2;0.187315,MA0099.2;0.139496,MA0079.2;0.0418452,MA0102.2;0.922526,MA0258.1;0.170584,MA0259.1;0.739179,MA0442.1;0
}}
}}

Revision as of 19:07, 22 January 2013


Full id: C375_optic_Cardiac_occipital_hippocampus_amygdala_heart_vagina



Phase1 CAGE Peaks

Hg19::chr10:23728870..23728914,-p@chr10:23728870..23728914
-
Hg19::chr14:64194979..64194990,-p5@SGPP1
Hg19::chr15:28878244..28878278,+p3@HERC2P9
Hg19::chr15:59203645..59203660,+p1@ENST00000460205
Hg19::chr18:74691000..74691005,-p@chr18:74691000..74691005
-
Hg19::chr18:77772838..77772849,+p1@ENST00000496399
Hg19::chr19:22877694..22877711,-p@chr19:22877694..22877711
-
Hg19::chr19:24186022..24186033,-p@chr19:24186022..24186033
-
Hg19::chr19:36369966..36369979,+p@chr19:36369966..36369979
+
Hg19::chr1:6663197..6663214,+p@chr1:6663197..6663214
+
Hg19::chr20:3052264..3052270,+p1@OXT
Hg19::chr20:3065362..3065375,-p1@AVP
Hg19::chr20:56423415..56423424,+p@chr20:56423415..56423424
+
Hg19::chr2:133013437..133013446,-p@chr2:133013437..133013446
-
Hg19::chr4:41216423..41216432,+p@chr4:41216423..41216432
+
Hg19::chr4:79860452..79860464,+p@chr4:79860452..79860464
+
Hg19::chr5:149681987..149681999,+p@chr5:149681987..149681999
+
Hg19::chr6:3692134..3692138,-p@chr6:3692134..3692138
-
Hg19::chr7:100231306..100231312,+p@chr7:100231306..100231312
+
Hg19::chr7:143208421..143208425,-p1@OR10AC1P
Hg19::chr7:148638615..148638633,+p1@RNY5
Hg19::chr7:22158177..22158186,-p@chr7:22158177..22158186
-
Hg19::chr8:22411813..22411825,+p55@SORBS3
Hg19::chr8:56755058..56755080,-p@chr8:56755058..56755080
-
Hg19::chr9:102693980..102693990,+p@chr9:102693980..102693990
+
Hg19::chr9:139740358..139740365,+p@chr9:139740358..139740365
+
Hg19::chr9:79186715..79186726,+p@chr9:79186715..79186726
+
Hg19::chrX:39548044..39548047,+p@chrX:39548044..39548047
+
Hg19::chrY:10035184..10035200,+p@chrY:10035184..10035200
+


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

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0031895V1B vasopressin receptor binding6.82805122742316e-07
GO:0031855oxytocin receptor binding6.82805122742316e-07
GO:0050891body fluid osmoregulation6.82805122742316e-07
GO:0031893vasopressin receptor binding1.02416748363524e-06
GO:0005185neurohypophyseal hormone activity1.02416748363524e-06
GO:0031894V1A vasopressin receptor binding1.02416748363524e-06
GO:0018987osmoregulation8.19173195646287e-06
GO:0005184neuropeptide hormone activity0.000135030968425998
GO:0001664G-protein-coupled receptor binding0.00121415974217814
GO:0050878regulation of body fluid levels0.00157986801149862
GO:0042392sphingosine-1-phosphate phosphatase activity0.00210868843860719
GO:0030816positive regulation of cAMP metabolic process0.00226678572039262
GO:0006670sphingosine metabolic process0.00226678572039262
GO:0006667sphinganine metabolic process0.00226678572039262
GO:0030804positive regulation of cyclic nucleotide biosynthetic process0.00226678572039262
GO:0045981positive regulation of nucleotide metabolic process0.00226678572039262
GO:0030819positive regulation of cAMP biosynthetic process0.00226678572039262
GO:0006668sphinganine-1-phosphate metabolic process0.00226678572039262
GO:0030810positive regulation of nucleotide biosynthetic process0.00226678572039262
GO:0030801positive regulation of cyclic nucleotide metabolic process0.00226678572039262
GO:0005179hormone activity0.00226678572039262
GO:0051496positive regulation of stress fiber formation0.00289919055618893
GO:0051495positive regulation of cytoskeleton organization and biogenesis0.00289919055618893
GO:0032233positive regulation of actin filament bundle formation0.00289919055618893
GO:0048878chemical homeostasis0.00368039417526195
GO:0030817regulation of cAMP biosynthetic process0.0039985303853693
GO:0003091renal water homeostasis0.0039985303853693
GO:0030146diuresis0.0039985303853693
GO:0017166vinculin binding0.0039985303853693
GO:0030802regulation of cyclic nucleotide biosynthetic process0.00409243273910375
GO:0051492regulation of stress fiber formation0.00409243273910375
GO:0030808regulation of nucleotide biosynthetic process0.00409243273910375
GO:0032231regulation of actin filament bundle formation0.00409243273910375
GO:0030814regulation of cAMP metabolic process0.00409243273910375
GO:0030799regulation of cyclic nucleotide metabolic process0.00438718911543101
GO:0043149stress fiber formation0.00438718911543101
GO:0030104water homeostasis0.00438718911543101
GO:0007567parturition0.00475659573642449
GO:0043410positive regulation of MAPKKK cascade0.00475659573642449
GO:0003014renal system process0.00521716056497323
GO:0042592homeostatic process0.00552056104825354
GO:0006140regulation of nucleotide metabolic process0.00552056104825354
GO:0006833water transport0.00579633313918826
GO:0042044fluid transport0.00579633313918826
GO:0051130positive regulation of cellular component organization and biogenesis0.00721225905871929
GO:0043408regulation of MAPKKK cascade0.00755909920924628
GO:0042310vasoconstriction0.00789113665704299
GO:0007589fluid secretion0.00869181253526654
GO:0051017actin filament bundle formation0.00880731442979931
GO:0006171cAMP biosynthetic process0.00880731442979931
GO:0046058cAMP metabolic process0.00999665889986511
GO:0005925focal adhesion0.015011611682781
GO:0000267cell fraction0.015011611682781
GO:0046519sphingoid metabolic process0.015011611682781
GO:0005924cell-substrate adherens junction0.015435742176374
GO:0065008regulation of biological quality0.015435742176374
GO:0048522positive regulation of cellular process0.015435742176374
GO:0009190cyclic nucleotide biosynthetic process0.015435742176374
GO:0030055cell-matrix junction0.015435742176374
GO:0007015actin filament organization0.015435742176374
GO:0007588excretion0.015435742176374
GO:0035150regulation of tube size0.015435742176374
GO:0050880regulation of blood vessel size0.015435742176374
GO:0003018vascular process in circulatory system0.0155556468794977
GO:0005102receptor binding0.0162484472590287
GO:0048518positive regulation of biological process0.0167667441072256
GO:0009187cyclic nucleotide metabolic process0.0172727118713187
GO:0005912adherens junction0.0183769505943518
GO:0051493regulation of cytoskeleton organization and biogenesis0.0185114408611819
GO:0033043regulation of organelle organization and biogenesis0.0185114408611819
GO:0006950response to stress0.020506881207144
GO:0006665sphingolipid metabolic process0.0218422042088823
GO:0009891positive regulation of biosynthetic process0.0221746544257607
GO:0035239tube morphogenesis0.0258463519980026
GO:0005200structural constituent of cytoskeleton0.0258463519980026
GO:0016323basolateral plasma membrane0.0258463519980026
GO:0051128regulation of cellular component organization and biogenesis0.0299926897886429
GO:0031589cell-substrate adhesion0.0304923716384611
GO:0007165signal transduction0.0306487966665124
GO:0035295tube development0.033750160244109
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0361665252615426
GO:0007154cell communication0.0369427395620263
GO:0000165MAPKKK cascade0.0416447144289407
GO:0009967positive regulation of signal transduction0.0419663592318712
GO:0008015blood circulation0.0428525175398149
GO:0003013circulatory system process0.0428525175398149



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism4.38e-77114
neural tube9.25e-2756
neural rod9.25e-2756
future spinal cord9.25e-2756
neural keel9.25e-2756
regional part of nervous system1.38e-2453
regional part of brain1.38e-2453
regional part of forebrain1.01e-2241
forebrain1.01e-2241
anterior neural tube1.01e-2241
future forebrain1.01e-2241
brain grey matter2.83e-2234
gray matter2.83e-2234
neural plate3.93e-2282
presumptive neural plate3.93e-2282
neurectoderm1.34e-2086
brain8.37e-2068
future brain8.37e-2068
telencephalon1.11e-1934
central nervous system2.38e-1981
regional part of telencephalon2.64e-1932
nervous system8.32e-1889
cerebral hemisphere3.02e-1732
pre-chordal neural plate7.09e-1761
ecto-epithelium2.32e-16104
structure with developmental contribution from neural crest3.69e-15132
organ system subdivision5.66e-15223
regional part of cerebral cortex8.66e-1522
cerebral cortex1.28e-1225
pallium1.28e-1225
neural nucleus2.02e-129
nucleus of brain2.02e-129
neocortex6.81e-1220
anatomical cluster3.71e-11373
anatomical conduit2.25e-10240
ectoderm-derived structure1.21e-09171
ectoderm1.21e-09171
presumptive ectoderm1.21e-09171
tube1.46e-09192
basal ganglion2.46e-099
nuclear complex of neuraxis2.46e-099
aggregate regional part of brain2.46e-099
collection of basal ganglia2.46e-099
cerebral subcortex2.46e-099
multi-tissue structure4.45e-09342
telencephalic nucleus5.82e-097
organ1.22e-08503
embryonic structure4.38e-08564
brainstem4.39e-086
organ part4.89e-08218
germ layer7.83e-08560
germ layer / neural crest7.83e-08560
embryonic tissue7.83e-08560
presumptive structure7.83e-08560
germ layer / neural crest derived structure7.83e-08560
epiblast (generic)7.83e-08560
embryo1.55e-07592
male genital duct3.13e-073
internal male genitalia3.13e-073
developing anatomical structure3.46e-07581
cardiac chamber3.67e-073
multi-cellular organism8.35e-07656


Overrepresented TFBS (DNA) motifs on this co-expression cluster<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)
MA0003.12.92043
MA0004.10.68402
MA0006.10.14464
MA0007.10.639929
MA0009.10.429031
MA0014.10.500568
MA0017.10.185458
MA0019.10.188957
MA0024.10.9086
MA0025.10.544326
MA0027.11.97447
MA0028.10.160829
MA0029.10.358654
MA0030.10.349473
MA0031.10.809566
MA0038.10.483171
MA0040.10.363365
MA0041.10.111817
MA0042.10.65234
MA0043.10.429296
MA0046.10.419892
MA0048.11.12026
MA0050.10.654418
MA0051.10.476736
MA0052.11.70896
MA0055.11.07853
MA0056.10
MA0057.10.143357
MA0058.10.810579
MA0059.10.464811
MA0060.10.0102756
MA0061.10.620016
MA0063.10
MA0066.10.483822
MA0067.10.711124
MA0068.10.451179
MA0069.10.416668
MA0070.10.407339
MA0071.10.839953
MA0072.10.403605
MA0073.10.000275135
MA0074.11.48035
MA0076.10.065346
MA0077.10.397221
MA0078.10.633683
MA0081.10.212556
MA0083.11.11054
MA0084.10.887042
MA0087.10.401577
MA0088.10.42613
MA0089.10
MA0090.10.0714597
MA0091.10.3381
MA0092.10.0849313
MA0093.10.617114
MA0095.10
MA0098.10
MA0100.10.168841
MA0101.10.627154
MA0103.10.318372
MA0105.11.21636
MA0106.10.18641
MA0107.10.414244
MA0108.20.804276
MA0109.10
MA0111.10.955933
MA0113.10.573327
MA0114.10.65856
MA0115.10.640975
MA0116.10.423674
MA0117.11.16571
MA0119.11.15535
MA0122.10.483183
MA0124.10.60338
MA0125.10.528543
MA0130.10
MA0131.10.663587
MA0132.10
MA0133.10
MA0135.10.454747
MA0136.10.164568
MA0139.10.355529
MA0140.10.421202
MA0141.10.80074
MA0142.11.38281
MA0143.10.573609
MA0144.10.0711193
MA0145.10.685149
MA0146.11.57099
MA0147.11.03959
MA0148.10.743891
MA0149.10.129939
MA0062.20.00628534
MA0035.20.135068
MA0039.20.0326666
MA0138.21.85435
MA0002.20.124839
MA0137.20.167559
MA0104.20.745965
MA0047.20.528161
MA0112.21.07456
MA0065.20.516863
MA0150.10.24291
MA0151.10
MA0152.10.430874
MA0153.10.513757
MA0154.11.18887
MA0155.10.780312
MA0156.10.0444235
MA0157.10.708688
MA0158.10
MA0159.10.435001
MA0160.10.390619
MA0161.10
MA0162.10.0749742
MA0163.10.681668
MA0164.10.205602
MA0080.20.0373957
MA0018.20.187315
MA0099.20.139496
MA0079.20.0418452
MA0102.20.922526
MA0258.10.170584
MA0259.10.739179
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
POLR3G#10622174.98052738336710.01325227943238470.046880561312835



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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