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Coexpression cluster:C801: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.280498,0.602335,0.273994,0.404877,0.668883,1.04099,0.474413,0.855419,0.429396,0.230076,0.375531,0.515448,0.107365,0.46359,0.236531,1.31515,0.68716,0.559826,0.748636,0.708167,0.274046,1.17138,0.396189,0.233338,0.844704,0.537051,0.641011,0.39419,0.240354,0.590419,0.355553,0.722879,0.495657,0.352585,0.20845,0.568934,0.20579,0.404426,1.04488,0.395523,0.207288,0.340749,1.7121,0.235234,0.0391382,0.301189,0.47544,0.365597,1.6288,0.675323,0.550604,0.486559,0.214602,0.797754,0.947672,0.466348,0.244111,0.435652,1.47951,1.10913,0.762758,0.477672,0.848838,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.144996,0.0579262,0.945703,0.104203,0.0955465,2.08656,0.644006,0.709631,5.15302,0.764106,0.659298,0.49429,0.439665,0.89511,0.0510741,0.0463436,0.971783,0.575506,1.4989,1.12715,0.868602,0.739223,0.171001,0.238337,2.30812,0.368981,0.780743,0.579925,0.244963,1.65658,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.22412,0.283874,0.772599,0.269151,0.384185,1.07963,0.204477,0.0648813,0.354459,0.624851,0.515375,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.182384,0.869279,1.67994,0.993705,0.50181,1.13991,0.553614,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.337738,0.168379,0.052013,0.0287097,0.869654,2.596,0.477214,1.26919,0.560015,0.64107,0.844822,0.28899,1.05976,0.851493,0.708865,0.291837,0.633206,0.493542,0.479645,2.07178,2.01872
|tfbs_overrepresentation_for_novel_motifs=0.280498,0.602335,0.273994,0.404877,0.668883,1.04099,0.474413,0.855419,0.429396,0.230076,0.375531,0.515448,0.107365,0.46359,0.236531,1.31515,0.68716,0.559826,0.748636,0.708167,0.274046,1.17138,0.396189,0.233338,0.844704,0.537051,0.641011,0.39419,0.240354,0.590419,0.355553,0.722879,0.495657,0.352585,0.20845,0.568934,0.20579,0.404426,1.04488,0.395523,0.207288,0.340749,1.7121,0.235234,0.0391382,0.301189,0.47544,0.365597,1.6288,0.675323,0.550604,0.486559,0.214602,0.797754,0.947672,0.466348,0.244111,0.435652,1.47951,1.10913,0.762758,0.477672,0.848838,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.144996,0.0579262,0.945703,0.104203,0.0955465,2.08656,0.644006,0.709631,5.15302,0.764106,0.659298,0.49429,0.439665,0.89511,0.0510741,0.0463436,0.971783,0.575506,1.4989,1.12715,0.868602,0.739223,0.171001,0.238337,2.30812,0.368981,0.780743,0.579925,0.244963,1.65658,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.22412,0.283874,0.772599,0.269151,0.384185,1.07963,0.204477,0.0648813,0.354459,0.624851,0.515375,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.182384,0.869279,1.67994,0.993705,0.50181,1.13991,0.553614,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.337738,0.168379,0.052013,0.0287097,0.869654,2.596,0.477214,1.26919,0.560015,0.64107,0.844822,0.28899,1.05976,0.851493,0.708865,0.291837,0.633206,0.493542,0.479645,2.07178,2.01872
|tfbs_overrepresentation_jaspar=MA0003.1;0.000221536,MA0004.1;0.380329,MA0006.1;0.236135,MA0007.1;0.363007,MA0009.1;0.828613,MA0014.1;0.0679667,MA0017.1;0.744788,MA0019.1;0.520264,MA0024.1;0.725404,MA0025.1;0.960689,MA0027.1;2.43535,MA0028.1;0.25013,MA0029.1;0.744375,MA0030.1;0.733118,MA0031.1;1.60734,MA0038.1;0.477043,MA0040.1;0.750125,MA0041.1;0.397617,MA0042.1;0.367902,MA0043.1;0.828925,MA0046.1;0.817858,MA0048.1;0.0613414,MA0050.1;0.368721,MA0051.1;0.473017,MA0052.1;0.753928,MA0055.1;0.577037,MA0056.1;0,MA0057.1;0.0580131,MA0058.1;0.293055,MA0059.1;0.291897,MA0060.1;0.138988,MA0061.1;0.118318,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;0.0911063,MA0069.1;0.814052,MA0070.1;0.803003,MA0071.1;1.12112,MA0072.1;0.798564,MA0073.1;0.137855,MA0074.1;0.4723,MA0076.1;0.307383,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;0.292043,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;0.300184,MA0089.1;0,MA0090.1;0.857892,MA0091.1;0.382762,MA0092.1;0.918839,MA0093.1;0.238771,MA0095.1;0,MA0098.1;0,MA0100.1;1.2287,MA0101.1;0.678051,MA0103.1;0.228129,MA0105.1;0.0508589,MA0106.1;3.26589,MA0107.1;0.179177,MA0108.2;0.666881,MA0109.1;0,MA0111.1;0.33284,MA0113.1;0.532314,MA0114.1;0.51954,MA0115.1;1.06753,MA0116.1;0.536665,MA0117.1;0.865782,MA0119.1;0.277531,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;0.585907,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;0.109245,MA0140.1;0.437738,MA0141.1;0.789887,MA0142.1;0.638837,MA0143.1;0.532484,MA0144.1;0.163394,MA0145.1;0.14293,MA0146.1;0.243477,MA0147.1;0.184931,MA0148.1;0.403564,MA0149.1;0.428597,MA0062.2;0.114378,MA0035.2;0.437071,MA0039.2;0.233545,MA0138.2;0.569505,MA0002.2;0.407187,MA0137.2;0.255808,MA0104.2;0.138396,MA0047.2;0.504873,MA0112.2;0.573053,MA0065.2;0.963081,MA0150.1;0.315136,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;0.414714,MA0155.1;0.866026,MA0156.1;0.257809,MA0157.1;0.612166,MA0158.1;0,MA0159.1;1.04074,MA0160.1;1.88551,MA0161.1;0,MA0162.1;0.403951,MA0163.1;0.162989,MA0164.1;0.544294,MA0080.2;0.238846,MA0018.2;0.517858,MA0099.2;1.12985,MA0079.2;0.48867,MA0102.2;1.36707,MA0258.1;1.47203,MA0259.1;0.191914,MA0442.1;0
}}
}}

Revision as of 19:27, 22 January 2013


Full id: C801_substantia_spinal_medulla_retina_pineal_penis_tongue



Phase1 CAGE Peaks

Hg19::chr11:58390132..58390156,+p1@CNTF
Hg19::chr11:58390160..58390175,+p2@CNTF
Hg19::chr17:79106634..79106641,-p@chr17:79106634..79106641
-
Hg19::chr1:161274636..161274641,-p@chr1:161274636..161274641
-
Hg19::chr1:24915935..24915949,+p2@C1orf130
Hg19::chr1:24915966..24915971,+p5@C1orf130
Hg19::chr1:24915973..24915984,+p3@C1orf130
Hg19::chr20:52612624..52612642,-p5@BCAS1
Hg19::chrX:100489564..100489583,+p@chrX:100489564..100489583
+
Hg19::chrX:100489588..100489605,+p@chrX:100489588..100489605
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism9.70e-34114
posterior neural tube1.08e-2515
chordal neural plate1.08e-2515
brainstem1.19e-256
spinal cord3.95e-203
dorsal region element3.95e-203
dorsum3.95e-203
medulla oblongata8.42e-203
myelencephalon8.42e-203
future myelencephalon8.42e-203
open tracheal system trachea1.71e-132
throat2.99e-132
segmental subdivision of hindbrain9.65e-1312
hindbrain9.65e-1312
presumptive hindbrain9.65e-1312
segmental subdivision of nervous system9.58e-1213
neural plate4.66e-1082
presumptive neural plate4.66e-1082
structure with developmental contribution from neural crest6.79e-10132
neurectoderm1.77e-0986
tongue2.33e-093
gustatory system2.33e-093
future tongue2.33e-093
neural tube3.31e-0956
neural rod3.31e-0956
future spinal cord3.31e-0956
neural keel3.31e-0956
compound organ5.78e-0968
valve7.01e-093
cardiac mesenchyme7.01e-093
cardial valve7.01e-093
tunica intima7.01e-093
heart layer7.01e-093
endocardium7.01e-093
endocardial cushion7.01e-093
presumptive endocardium7.01e-093
pons7.91e-093
central nervous system1.95e-0881
substantia nigra6.59e-081
midbrain nucleus6.59e-081
regional part of midbrain6.59e-081
midbrain6.59e-081
presumptive midbrain6.59e-081
midbrain neural tube6.59e-081
ectoderm-derived structure9.92e-08171
ectoderm9.92e-08171
presumptive ectoderm9.92e-08171
penis1.10e-071
intromittent organ1.10e-071
lateral plate mesenchyme1.10e-071
undifferentiated genital tubercle1.10e-071
somatopleure1.10e-071
dura mater1.61e-071
future meninx1.61e-071
ectomeninx1.61e-071
future dura mater1.61e-071
ecto-epithelium2.00e-07104
nervous system2.16e-0789
pulmonary valve2.50e-071
semi-lunar valve2.50e-071
epididymis2.66e-071
mitral valve3.20e-071
tonsil3.62e-071
mucosa-associated lymphoid tissue3.62e-071
lymphoid tissue3.62e-071
tonsillar ring3.62e-071


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)
MA0003.10.000221536
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.0679667
MA0017.10.744788
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.11.60734
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.577037
MA0056.10
MA0057.10.0580131
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.11.12112
MA0072.10.798564
MA0073.10.137855
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.300184
MA0089.10
MA0090.10.857892
MA0091.10.382762
MA0092.10.918839
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.11.2287
MA0101.10.678051
MA0103.10.228129
MA0105.10.0508589
MA0106.13.26589
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.51954
MA0115.11.06753
MA0116.10.536665
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.10.437738
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.14293
MA0146.10.243477
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.233545
MA0138.20.569505
MA0002.20.407187
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.573053
MA0065.20.963081
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.414714
MA0155.10.866026
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.04074
MA0160.11.88551
MA0161.10
MA0162.10.403951
MA0163.10.162989
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.21.12985
MA0079.20.48867
MA0102.21.36707
MA0258.11.47203
MA0259.10.191914
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

No analysis results for this cluster

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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