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Coexpression cluster:C668: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.13027,0.193861,1.10792,0.320418,0.17087,0.319017,0.385011,0.0904943,0.0889928,0.120648,0.293498,0.423573,0.0649383,0.37489,1.55512,0.187326,0.587543,4.10207,0.0716493,0.74987,0.585797,0.148689,1.51832,1.53916,0.238419,0.443987,0.0543847,0.310589,0.173154,0.399779,1.38383,0.622056,0.355848,0.234859,0.145955,3.11418,0.143715,0.320003,0.127608,0.270447,0.445225,0.261903,1.5935,0.973137,1.04897,0.226447,0.385972,0.284438,4.58507,0.173249,2.01716,0.396393,2.19882,2.79123,0.841347,0.377467,0.176395,0.348876,0.0468732,0.919233,0.660716,0.388062,0.0892869,0.561703,0.403967,0.529794,0.927044,1.28869,0.612294,1.12869,0.251183,0.0939573,0.542218,1.95781,0.0625815,0.787787,2.10545,0.546008,0.609242,0.233499,0.932155,0.560705,0.403653,0.0921949,0.789807,0.00329133,0.0226931,0.0447464,0.480498,1.38705,1.01818,0.763867,0.637885,1.21732,0.171417,1.27368,0.0708422,0.67819,0.484706,0.0378976,0.12852,0.632556,0.672898,0.590971,0.519171,1.43641,2.41062,0.371864,0.238217,0.15924,0.211112,0.670274,0.575539,0.301413,0.971251,0.439271,0.00477951,0.274314,0.527634,0.116746,0.831412,2.08886,0.316671,0.413695,1.0796,0.546713,0.379419,0.642598,9.6494,0.124214,0.76453,1.39251,0.886589,0.410725,1.03079,0.0417786,0.270369,0.311068,0.989273,1.83943,1.43902,0.95284,0.38094,0.674844,0.52079,0.341558,0.505455,1.68078,0.259186,0.112739,0.0262543,0.0123511,0.764896,0.0843101,2.67451,1.15881,0.465765,1.50139,0.238466,0.21563,0.951654,0.747146,0.608503,3.39155,0.535644,1.04011,0.10496,0.383837,0.000163658
|tfbs_overrepresentation_jaspar=MA0003.1;2.27829e-05,MA0004.1;0.297884,MA0006.1;0.169524,MA0007.1;0.282081,MA0009.1;0.724811,MA0014.1;0.000874969,MA0017.1;6.95615,MA0019.1;0.428118,MA0024.1;0.6245,MA0025.1;0.854131,MA0027.1;2.32165,MA0028.1;0.181601,MA0029.1;0.642879,MA0030.1;0.63197,MA0031.1;0.570886,MA0038.1;0.387473,MA0040.1;0.648455,MA0041.1;0.313738,MA0042.1;0.286538,MA0043.1;0.725115,MA0046.1;0.714324,MA0048.1;0.565955,MA0050.1;0.287284,MA0051.1;0.383704,MA0052.1;0.652145,MA0055.1;0.083823,MA0056.1;0,MA0057.1;0.861654,MA0058.1;0.219229,MA0059.1;0.218203,MA0060.1;0.2996,MA0061.1;0.0732084,MA0063.1;0,MA0066.1;0.387854,MA0067.1;1.03434,MA0068.1;0.0529803,MA0069.1;0.710614,MA0070.1;0.69985,MA0071.1;0.930644,MA0072.1;0.695528,MA0073.1;0.000252324,MA0074.1;0.383033,MA0076.1;0.231962,MA0077.1;0.688123,MA0078.1;0.473657,MA0081.1;0.218332,MA0083.1;0.732051,MA0084.1;1.21913,MA0087.1;0.693179,MA0088.1;0.0135703,MA0089.1;0,MA0090.1;2.74676,MA0091.1;4.06156,MA0092.1;0.268302,MA0093.1;0.171791,MA0095.1;0,MA0098.1;0,MA0100.1;0.399896,MA0101.1;0.517741,MA0103.1;0.948111,MA0105.1;0.491866,MA0106.1;0.424592,MA0107.1;0.77236,MA0108.2;0.568002,MA0109.1;0,MA0111.1;0.254772,MA0113.1;0.439505,MA0114.1;7.37172,MA0115.1;5.15773,MA0116.1;0.123927,MA0117.1;0.76111,MA0119.1;0.205526,MA0122.1;0.786181,MA0124.1;0.918678,MA0125.1;0.83671,MA0130.1;0,MA0131.1;0.490408,MA0132.1;0,MA0133.1;0,MA0135.1;0.754112,MA0136.1;0.393782,MA0139.1;0.0663461,MA0140.1;0.350813,MA0141.1;2.56169,MA0142.1;0.541045,MA0143.1;0.439666,MA0144.1;0.108694,MA0145.1;0.0164225,MA0146.1;0.0179216,MA0147.1;0.126316,MA0148.1;0.319209,MA0149.1;0.342334,MA0062.2;0.0702147,MA0035.2;0.350194,MA0039.2;0.00699112,MA0138.2;0.474787,MA0002.2;0.588143,MA0137.2;0.186529,MA0104.2;0.088751,MA0047.2;0.413608,MA0112.2;0.0689988,MA0065.2;0.953721,MA0150.1;1.24823,MA0151.1;0,MA0152.1;0.938262,MA0153.1;0.820317,MA0154.1;1.13157,MA0155.1;0.0132945,MA0156.1;0.18827,MA0157.1;0.515488,MA0158.1;0,MA0159.1;0.126752,MA0160.1;0.332385,MA0161.1;0,MA0162.1;0.00205586,MA0163.1;0.02611,MA0164.1;0.450848,MA0080.2;0.171855,MA0018.2;0.425847,MA0099.2;0.356906,MA0079.2;0.00203337,MA0102.2;1.25596,MA0258.1;0.102521,MA0259.1;0.132107,MA0442.1;0
}}
}}

Revision as of 19:21, 22 January 2013


Full id: C668_lymphangiectasia_lymph_submaxillary_appendix_vein_CD19_lymphoma



Phase1 CAGE Peaks

Hg19::chr2:89156701..89156711,-p@chr2:89156701..89156711
-
Hg19::chr2:89156772..89156782,-p@chr2:89156772..89156782
-
Hg19::chr2:89156903..89156965,+p1@CU688247
p1@CU689025
p1@CU689831
p1@CU689833
p1@CU689835
p1@CU691143
Hg19::chr2:89156917..89156926,-p7@AJ294735
Hg19::chr2:89156940..89156955,-p6@AJ294735
Hg19::chr2:89156976..89157016,+p4@CU688247
p4@CU689025
p4@CU689831
p4@CU689833
p4@CU689835
p4@CU691143
Hg19::chr2:89156995..89157014,-p4@AJ294735
Hg19::chr2:89157015..89157033,-p5@AJ294735
Hg19::chr2:89157041..89157057,-p3@AJ294735
Hg19::chr2:89157058..89157093,-p1@AJ294735
Hg19::chr2:89157095..89157160,-p2@AJ294735
Hg19::chr2:89157161..89157206,-p1@IGKC
Hg19::chr3:186714356..186714377,+p6@ST6GAL1


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:0006955immune response0.00220245711669294
GO:0002376immune system process0.00220245711669294
GO:0003835beta-galactoside alpha-2,6-sialyltransferase activity0.00765268573207231
GO:0009311oligosaccharide metabolic process0.0315506045610944
GO:0032393MHC class I receptor activity0.0363138866499496
GO:0008373sialyltransferase activity0.0363138866499496
GO:0030173integral to Golgi membrane0.0477293874861276
GO:0031228intrinsic to Golgi membrane0.0477293874861276
GO:0006959humoral immune response0.0477293874861276



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>disease_data<br>

Cell Type
Ontology termp-valuen
B cell5.82e-3214
lymphocyte of B lineage8.26e-3024
pro-B cell8.26e-3024
lymphoid lineage restricted progenitor cell3.15e-1452
lymphocyte7.27e-1453
common lymphoid progenitor7.27e-1453
nucleate cell3.52e-1355
nongranular leukocyte8.90e-09115
single nucleate cell1.24e-073
mononuclear cell1.24e-073
leukocyte3.43e-07136
Uber Anatomy
Ontology termp-valuen
adult organism7.27e-33114
blood4.63e-1215
haemolymphatic fluid4.63e-1215
organism substance4.63e-1215
major salivary gland8.60e-072
Disease
Ontology termp-valuen
lymphoma7.45e-0910


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)
MA0003.12.27829e-05
MA0004.10.297884
MA0006.10.169524
MA0007.10.282081
MA0009.10.724811
MA0014.10.000874969
MA0017.16.95615
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.10.565955
MA0050.10.287284
MA0051.10.383704
MA0052.10.652145
MA0055.10.083823
MA0056.10
MA0057.10.861654
MA0058.10.219229
MA0059.10.218203
MA0060.10.2996
MA0061.10.0732084
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.10.0529803
MA0069.10.710614
MA0070.10.69985
MA0071.10.930644
MA0072.10.695528
MA0073.10.000252324
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.218332
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.0135703
MA0089.10
MA0090.12.74676
MA0091.14.06156
MA0092.10.268302
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.517741
MA0103.10.948111
MA0105.10.491866
MA0106.10.424592
MA0107.10.77236
MA0108.20.568002
MA0109.10
MA0111.10.254772
MA0113.10.439505
MA0114.17.37172
MA0115.15.15773
MA0116.10.123927
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.0663461
MA0140.10.350813
MA0141.12.56169
MA0142.10.541045
MA0143.10.439666
MA0144.10.108694
MA0145.10.0164225
MA0146.10.0179216
MA0147.10.126316
MA0148.10.319209
MA0149.10.342334
MA0062.20.0702147
MA0035.20.350194
MA0039.20.00699112
MA0138.20.474787
MA0002.20.588143
MA0137.20.186529
MA0104.20.088751
MA0047.20.413608
MA0112.20.0689988
MA0065.20.953721
MA0150.11.24823
MA0151.10
MA0152.10.938262
MA0153.10.820317
MA0154.11.13157
MA0155.10.0132945
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.10.126752
MA0160.10.332385
MA0161.10
MA0162.10.00205586
MA0163.10.02611
MA0164.10.450848
MA0080.20.171855
MA0018.20.425847
MA0099.20.356906
MA0079.20.00203337
MA0102.21.25596
MA0258.10.102521
MA0259.10.132107
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
POLR2A#5430132.147453176558074.83928878402115e-050.000840949220157046
POU2F2#5452128.405652976377713.58336042559485e-114.10804148725248e-09
TAF1#6872133.343046285745291.53362599454097e-078.60668271057841e-06



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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