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Coexpression cluster:C1485: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.97464,0.143275,2.90252,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.262261,4.61767,0.707204,0.635275,1.56773,0.391663,0.415981,0.889639,0.336106,0.236034,0.402028,0.436569,0.0880431,0.576478,0.387783,0.483957,11.819,0.202389,0.574247,1.81189,0.186644,1.31499,0.92701,1.48187,0.225641,1.67655,0.0334022,0.35388,0.585658,0.329602,1.28576,0.355745,3.25435,0.0979105,0.390088,0.0393783,2.05586,2.69274,2.29967,0.630853,0.396429,0.745008,0.675919,0.149032,2.29597,1.15929,0.653901,0.400834,0.62023,2.34444,1.50144,0.968558,0.666252,0.267534,2.00306,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,4.31841,0.275507,1.41895,1.15727,0.218784,0.206105,1.68655,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.181326,0.126687,2.31006,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,1.74379,0.44815,3.67893,0.430775,0.563054,1.29401,0.352243,0.800507,0.529546,0.824029,0.312699,1.14892,1.81315,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,1.30187,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,2.2813,4.17163,0.0926553,2.44691,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,5.22244,0.83286,0.683502,0.29379,0.661335,0.152397
|tfbs_overrepresentation_for_novel_motifs=1.97464,0.143275,2.90252,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.262261,4.61767,0.707204,0.635275,1.56773,0.391663,0.415981,0.889639,0.336106,0.236034,0.402028,0.436569,0.0880431,0.576478,0.387783,0.483957,11.819,0.202389,0.574247,1.81189,0.186644,1.31499,0.92701,1.48187,0.225641,1.67655,0.0334022,0.35388,0.585658,0.329602,1.28576,0.355745,3.25435,0.0979105,0.390088,0.0393783,2.05586,2.69274,2.29967,0.630853,0.396429,0.745008,0.675919,0.149032,2.29597,1.15929,0.653901,0.400834,0.62023,2.34444,1.50144,0.968558,0.666252,0.267534,2.00306,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,4.31841,0.275507,1.41895,1.15727,0.218784,0.206105,1.68655,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.181326,0.126687,2.31006,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,1.74379,0.44815,3.67893,0.430775,0.563054,1.29401,0.352243,0.800507,0.529546,0.824029,0.312699,1.14892,1.81315,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,1.30187,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,2.2813,4.17163,0.0926553,2.44691,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,5.22244,0.83286,0.683502,0.29379,0.661335,0.152397
|tfbs_overrepresentation_jaspar=MA0003.1;0.026277,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;1.56589,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.906394,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;3.5183,MA0056.1;0,MA0057.1;0.882847,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;4.7629,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00076337,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.830067,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;2.88836,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;2.62599,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;2.32339,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.00570825,MA0138.2;0.765223,MA0002.2;2.82381,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.0961854,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;2.38949,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.0383129,MA0163.1;0.0270301,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;1.42871,MA0102.2;1.58513,MA0258.1;0.788656,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:58, 22 January 2013


Full id: C1485_myeloma_putamen_caudate_nucleus_Dendritic_pons_Lymphatic



Phase1 CAGE Peaks

Hg19::chr20:9495321..9495340,+p8@LAMP5
Hg19::chr20:9495383..9495390,+p14@LAMP5
Hg19::chr20:9495392..9495403,+p9@LAMP5
Hg19::chr20:9495410..9495426,+p5@LAMP5
Hg19::chr20:9495430..9495472,+p2@LAMP5
Hg19::chr20:9495486..9495495,+p13@LAMP5


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

No GOStat results

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
plasmacytoid dendritic cell5.35e-073
Uber Anatomy
Ontology termp-valuen
neural tube6.21e-6156
neural rod6.21e-6156
future spinal cord6.21e-6156
neural keel6.21e-6156
central nervous system6.42e-5781
regional part of nervous system2.10e-5653
regional part of brain2.10e-5653
nervous system4.93e-5489
brain1.68e-4868
future brain1.68e-4868
regional part of forebrain1.24e-4441
forebrain1.24e-4441
anterior neural tube1.24e-4441
future forebrain1.24e-4441
neural plate6.54e-4482
presumptive neural plate6.54e-4482
adult organism7.54e-42114
neurectoderm4.12e-4186
telencephalon3.49e-4034
brain grey matter4.96e-4034
gray matter4.96e-4034
cerebral hemisphere7.76e-3832
regional part of telencephalon2.22e-3732
pre-chordal neural plate1.49e-3161
ecto-epithelium3.34e-31104
regional part of cerebral cortex1.11e-3022
neocortex1.72e-2720
ectoderm-derived structure1.60e-26171
ectoderm1.60e-26171
presumptive ectoderm1.60e-26171
cerebral cortex2.51e-2625
pallium2.51e-2625
structure with developmental contribution from neural crest1.25e-25132
organ system subdivision4.25e-23223
posterior neural tube9.11e-1715
chordal neural plate9.11e-1715
basal ganglion3.54e-169
nuclear complex of neuraxis3.54e-169
aggregate regional part of brain3.54e-169
collection of basal ganglia3.54e-169
cerebral subcortex3.54e-169
neural nucleus1.85e-159
nucleus of brain1.85e-159
anatomical cluster3.18e-13373
telencephalic nucleus6.37e-137
segmental subdivision of hindbrain1.42e-1212
hindbrain1.42e-1212
presumptive hindbrain1.42e-1212
segmental subdivision of nervous system2.03e-1113
tube2.44e-11192
anatomical conduit3.25e-11240
gyrus6.15e-116
brainstem1.18e-106
limbic system6.89e-105
parietal lobe2.32e-095
temporal lobe2.73e-096
corpus striatum7.90e-094
striatum7.90e-094
ventral part of telencephalon7.90e-094
future corpus striatum7.90e-094
regional part of metencephalon3.00e-089
metencephalon3.00e-089
future metencephalon3.00e-089
caudate-putamen4.87e-073
dorsal striatum4.87e-073


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)
MA0003.10.026277
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.11.56589
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.13.5183
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.14.7629
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.12.88836
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.12.62599
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.12.32339
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.22.82381
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.12.38949
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.21.42871
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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
PAX5#507966.669565531177831.13557256338955e-050.000289970814053401
REST#597869.650028716128021.23743801704917e-064.99176473783695e-05
SIN3A#2594265.408884726815143.99207083571449e-050.000743186962586783
SUZ12#23512650.11578091106296.2866744827465e-116.99226833124134e-09



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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