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Coexpression cluster:C3655: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.66899,0.869629,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,0.491742,1.84557,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,1.26332,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,1.44641,1.72524,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,0.977977,0.303648,0.381882,2.39382,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,1.68795,1.39614,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,1.54007,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.96295
|tfbs_overrepresentation_jaspar=MA0003.1;2.61626,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.24048,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;1.58389,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;2.37507,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0185922,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;1.35563,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.752137,MA0146.1;1.70974,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.141,MA0035.2;0.894194,MA0039.2;0.432958,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.838867,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.09178,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:31, 22 January 2013


Full id: C3655_mature_optic_corpus_spinal_globus_medulla_substantia



Phase1 CAGE Peaks

Hg19::chr17:48785216..48785291,-p1@ANKRD40
Hg19::chr1:149982554..149982573,-p3@OTUD7B
Hg19::chr8:27468717..27468788,-p3@CLU


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:0016235aggresome0.00953656411554144
GO:0016579protein deubiquitination0.00953656411554144
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.00953656411554144
GO:0016234inclusion body0.00953656411554144
GO:0031018endocrine pancreas development0.00953656411554144
GO:0031016pancreas development0.0132444480846854
GO:0048523negative regulation of cellular process0.020411819014579
GO:0048519negative regulation of biological process0.020411819014579
GO:0006958complement activation, classical pathway0.0238298294633898
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0238298294633898
GO:0035270endocrine system development0.0238298294633898
GO:0006956complement activation0.0238298294633898
GO:0002541activation of plasma proteins during acute inflammatory response0.0238298294633898
GO:0045597positive regulation of cell differentiation0.0250859676778148
GO:0016064immunoglobulin mediated immune response0.0250859676778148
GO:0019724B cell mediated immunity0.0250859676778148
GO:0048471perinuclear region of cytoplasm0.0250859676778148
GO:0051094positive regulation of developmental process0.0250859676778148
GO:0002253activation of immune response0.0250859676778148
GO:0002449lymphocyte mediated immunity0.0250859676778148
GO:0006959humoral immune response0.0250859676778148
GO:0002250adaptive immune response0.0250859676778148
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0250859676778148
GO:0002443leukocyte mediated immunity0.0250859676778148
GO:0002526acute inflammatory response0.0250859676778148
GO:0050778positive regulation of immune response0.0252832945456699
GO:0002684positive regulation of immune system process0.0252832945456699
GO:0050776regulation of immune response0.0256392892352884
GO:0002682regulation of immune system process0.0256392892352884
GO:0009968negative regulation of signal transduction0.0256392892352884
GO:0051240positive regulation of multicellular organismal process0.0256392892352884
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0256392892352884
GO:0002252immune effector process0.0256392892352884
GO:0045087innate immune response0.0256392892352884
GO:0048667neuron morphogenesis during differentiation0.0256392892352884
GO:0006979response to oxidative stress0.0256392892352884
GO:0048812neurite morphogenesis0.0256392892352884
GO:0000904cellular morphogenesis during differentiation0.0256392892352884
GO:0031175neurite development0.0256392892352884
GO:0004221ubiquitin thiolesterase activity0.0256392892352884
GO:0004843ubiquitin-specific protease activity0.0256392892352884
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0256392892352884
GO:0019783small conjugating protein-specific protease activity0.0256392892352884
GO:0045595regulation of cell differentiation0.0259559796898568
GO:0048666neuron development0.0271376199582455
GO:0006916anti-apoptosis0.0292989543931793
GO:0016790thiolester hydrolase activity0.0306942946902211
GO:0032990cell part morphogenesis0.0323298184570564
GO:0048858cell projection morphogenesis0.0323298184570564
GO:0030030cell projection organization and biogenesis0.0323298184570564
GO:0030182neuron differentiation0.0326252427686447
GO:0043066negative regulation of apoptosis0.0339849946966792
GO:0043069negative regulation of programmed cell death0.0339849946966792
GO:0008284positive regulation of cell proliferation0.0339849946966792
GO:0050793regulation of developmental process0.0339849946966792
GO:0048699generation of neurons0.0342236829839282
GO:0022008neurogenesis0.0363912961601846
GO:0051239regulation of multicellular organismal process0.0378030291928459
GO:0006954inflammatory response0.0390324614353745
GO:0008234cysteine-type peptidase activity0.0394324299568541
GO:0007243protein kinase cascade0.0487188432564292



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 organism3.14e-46114
neural tube2.41e-2656
neural rod2.41e-2656
future spinal cord2.41e-2656
neural keel2.41e-2656
nervous system2.82e-2689
central nervous system4.09e-2581
regional part of nervous system3.15e-2453
regional part of brain3.15e-2453
brain1.04e-2368
future brain1.04e-2368
neural plate2.33e-2082
presumptive neural plate2.33e-2082
neurectoderm3.47e-1986
regional part of forebrain1.37e-1841
forebrain1.37e-1841
anterior neural tube1.37e-1841
future forebrain1.37e-1841
structure with developmental contribution from neural crest1.48e-18132
anatomical cluster5.64e-18373
organ system subdivision1.12e-17223
brain grey matter1.73e-1634
gray matter1.73e-1634
telencephalon1.81e-1634
anatomical conduit2.73e-16240
regional part of telencephalon4.67e-1532
cerebral hemisphere5.35e-1532
ectoderm-derived structure1.49e-14171
ectoderm1.49e-14171
presumptive ectoderm1.49e-14171
pre-chordal neural plate1.52e-1361
ecto-epithelium3.43e-13104
tube4.97e-13192
multi-cellular organism2.45e-12656
multi-tissue structure1.22e-11342
cell layer1.61e-10309
cerebral cortex1.92e-1025
pallium1.92e-1025
epithelium2.25e-10306
regional part of cerebral cortex6.23e-1022
anatomical system1.79e-09624
anatomical group2.56e-09625
posterior neural tube5.73e-0915
chordal neural plate5.73e-0915
neocortex1.12e-0820
neural nucleus5.55e-089
nucleus of brain5.55e-089
basal ganglion8.35e-089
nuclear complex of neuraxis8.35e-089
aggregate regional part of brain8.35e-089
collection of basal ganglia8.35e-089
cerebral subcortex8.35e-089
segmental subdivision of nervous system1.13e-0713
organ1.41e-07503
segmental subdivision of hindbrain6.38e-0712
hindbrain6.38e-0712
presumptive hindbrain6.38e-0712


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)
MA0003.12.61626
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.12.37507
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BCLAF1#9774214.43509840674790.006201147435546130.0273809511275949
CEBPB#105137.971147625824820.001974187055288560.0115140515925214
ELK4#2005210.8237877723120.01091284719516480.0401906639472394
EP300#203336.77394172622320.003216880500103790.0167331299208258
GATA3#2625218.15767757147070.003944546819279620.018946995596686
MEF2C#4208227.54090299508270.001729119938369690.0106472234681559
RXRA#6256213.38307809275550.007196434429465730.0298261206944312
SIX5#147912211.3911435703060.009873820081429030.0370726163173845



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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