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{{Coexpression_clusters
{
|full_id=C342_xeroderma_b_B_splenic_plasma_Burkitt_thymus
|

Latest revision as of 11:20, 17 September 2013


Full id: C342_xeroderma_b_B_splenic_plasma_Burkitt_thymus



Phase1 CAGE Peaks

Hg19::chr10:73976884..73976894,-p5@ASCC1
Hg19::chr11:120484784..120484795,+p@chr11:120484784..120484795
+
Hg19::chr12:111106975..111106991,-p@chr12:111106975..111106991
-
Hg19::chr12:111107001..111107019,-p@chr12:111107001..111107019
-
Hg19::chr14:21134939..21134952,-p@chr14:21134939..21134952
-
Hg19::chr16:81844780..81844795,+p@chr16:81844780..81844795
+
Hg19::chr16:81844812..81844828,+p@chr16:81844812..81844828
+
Hg19::chr17:16875371..16875447,-p1@TNFRSF13B
Hg19::chr17:28539815..28539831,-p@chr17:28539815..28539831
-
Hg19::chr17:46189327..46189378,+p4@SNX11
Hg19::chr17:46189383..46189391,+p6@SNX11
Hg19::chr17:67513291..67513311,+p@chr17:67513291..67513311
+
Hg19::chr18:60825483..60825499,-p@chr18:60825483..60825499
-
Hg19::chr18:60984634..60984649,+p@chr18:60984634..60984649
+
Hg19::chr19:14721826..14721829,+p@chr19:14721826..14721829
+
Hg19::chr1:101838740..101838743,+p@chr1:101838740..101838743
+
Hg19::chr1:160616804..160616822,-p1@SLAMF1
Hg19::chr1:75198161..75198173,+p@chr1:75198161..75198173
+
Hg19::chr21:26797217..26797228,-p5@LINC00158
Hg19::chr21:26797257..26797267,-p7@LINC00158
Hg19::chr22:39843128..39843135,+p@chr22:39843128..39843135
+
Hg19::chr22:42834287..42834305,+p2@ENST00000428765
Hg19::chr2:242052105..242052116,-p12@PASK
Hg19::chr2:25585766..25585790,+p@chr2:25585766..25585790
+
Hg19::chr2:45006189..45006201,+p@chr2:45006189..45006201
+
Hg19::chr4:154410402..154410460,+p@chr4:154410402..154410460
+
Hg19::chr5:96267483..96267496,+p@chr5:96267483..96267496
+
Hg19::chr5:96267508..96267529,+p@chr5:96267508..96267529
+
Hg19::chr7:44500049..44500072,-p@chr7:44500049..44500072
-
Hg19::chr7:99809276..99809341,+p2@STAG3
Hg19::chr8:22559141..22559159,-p@chr8:22559141..22559159
-
Hg19::chr8:22576954..22576965,+p@chr8:22576954..22576965
+
Hg19::chrX:12884985..12885009,+p6@TLR7


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:0030889negative regulation of B cell proliferation0.0135934311345815
GO:0009986cell surface0.0135934311345815
GO:0035197siRNA binding0.0135934311345815
GO:0046649lymphocyte activation0.0135934311345815
GO:0045321leukocyte activation0.0135934311345815
GO:0001775cell activation0.0135934311345815
GO:0045359positive regulation of interferon-beta biosynthetic process0.0135934311345815
GO:0032608interferon-beta production0.0135934311345815
GO:0045357regulation of interferon-beta biosynthetic process0.0135934311345815
GO:0001782B cell homeostasis0.0135934311345815
GO:0045356positive regulation of interferon-alpha biosynthetic process0.0135934311345815
GO:0045350interferon-beta biosynthetic process0.0135934311345815
GO:0045354regulation of interferon-alpha biosynthetic process0.0135934311345815
GO:0032607interferon-alpha production0.0135934311345815
GO:0045349interferon-alpha biosynthetic process0.0135934311345815
GO:0050869negative regulation of B cell activation0.0135934311345815
GO:0045416positive regulation of interleukin-8 biosynthetic process0.0135934311345815
GO:0007130synaptonemal complex assembly0.0135934311345815
GO:0007129synapsis0.0144640387975788
GO:0032606interferon type I production0.0144640387975788
GO:0045414regulation of interleukin-8 biosynthetic process0.0144640387975788
GO:0045351interferon type I biosynthetic process0.0144640387975788
GO:0042228interleukin-8 biosynthetic process0.0144640387975788
GO:0045078positive regulation of interferon-gamma biosynthetic process0.0144640387975788
GO:0002260lymphocyte homeostasis0.0144640387975788
GO:0030888regulation of B cell proliferation0.0144640387975788
GO:0050794regulation of cellular process0.0144640387975788
GO:0002376immune system process0.0144640387975788
GO:0032637interleukin-8 production0.0144640387975788
GO:0050672negative regulation of lymphocyte proliferation0.0144640387975788
GO:0032945negative regulation of mononuclear cell proliferation0.0144640387975788
GO:0045072regulation of interferon-gamma biosynthetic process0.0152845094127478
GO:0000795synaptonemal complex0.0155828295736444
GO:0042095interferon-gamma biosynthetic process0.0155828295736444
GO:0001776leukocyte homeostasis0.0160671495404434
GO:0050789regulation of biological process0.0160671495404434
GO:0048872homeostasis of number of cells0.0165194171830189
GO:0051607defense response to virus0.0171554937858324
GO:0032609interferon-gamma production0.017565387589091
GO:0042100B cell proliferation0.017565387589091
GO:0004871signal transducer activity0.017565387589091
GO:0060089molecular transducer activity0.017565387589091
GO:0042127regulation of cell proliferation0.017565387589091
GO:0051250negative regulation of lymphocyte activation0.0175894684695822
GO:0003727single-stranded RNA binding0.0181021819400095
GO:0065007biological regulation0.0192416850047778
GO:0050864regulation of B cell activation0.0216552828916914
GO:0000794condensed nuclear chromosome0.0262791975789329
GO:0007127meiosis I0.0273988804587277
GO:0042108positive regulation of cytokine biosynthetic process0.0328333983870052
GO:0050670regulation of lymphocyte proliferation0.0328333983870052
GO:0032944regulation of mononuclear cell proliferation0.0328333983870052
GO:0008283cell proliferation0.0350210979489749
GO:0009897external side of plasma membrane0.0364814455963035
GO:0000793condensed chromosome0.0364814455963035
GO:0032943mononuclear cell proliferation0.0364814455963035
GO:0045727positive regulation of translation0.0364814455963035
GO:0046651lymphocyte proliferation0.0364814455963035
GO:0003725double-stranded RNA binding0.0364814455963035
GO:0007059chromosome segregation0.0392770992516106
GO:0042035regulation of cytokine biosynthetic process0.0392770992516106
GO:0031328positive regulation of cellular biosynthetic process0.0392770992516106
GO:0042113B cell activation0.0392944123856529
GO:0044454nuclear chromosome part0.041126194104434
GO:0042089cytokine biosynthetic process0.041126194104434
GO:0042107cytokine metabolic process0.041126194104434
GO:0051327M phase of meiotic cell cycle0.041126194104434
GO:0007126meiosis0.041126194104434
GO:0009891positive regulation of biosynthetic process0.041126194104434
GO:0051321meiotic cell cycle0.041126194104434
GO:0048522positive regulation of cellular process0.0420029648832667
GO:0051249regulation of lymphocyte activation0.0427493305344138
GO:0003723RNA binding0.0427493305344138
GO:0050865regulation of cell activation0.0436126357869517
GO:0007154cell communication0.0436126357869517
GO:0051247positive regulation of protein metabolic process0.0452925725332192
GO:0048518positive regulation of biological process0.0474896897675038



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>

Uber Anatomy
Ontology termp-valuen
hemopoietic organ9.59e-397
immune organ9.59e-397
spleen1.32e-333
gastrointestinal system mesentery1.32e-333
stomach region1.32e-333
mesentery1.32e-333
gastrointestinal system serosa1.32e-333
mesentery of stomach1.32e-333
gut mesentery1.32e-333
dorsal mesentery1.32e-333
dorsal mesogastrium1.32e-333
peritoneal cavity1.32e-333
spleen primordium1.32e-333
stomach5.05e-138
food storage organ5.05e-138
vermiform appendix1.96e-121
caecum1.96e-121
midgut1.96e-121
tonsil2.46e-121
mucosa-associated lymphoid tissue2.46e-121
lymphoid tissue2.46e-121
tonsillar ring2.46e-121
thymus1.05e-114
hemolymphoid system gland1.05e-114
thymic region1.05e-114
pharyngeal gland1.05e-114
thymus primordium1.05e-114
chordate pharynx2.47e-1010
pharyngeal region of foregut2.47e-1010
pharynx1.91e-0911
mixed endoderm/mesoderm-derived structure2.40e-0929
cavity lining7.26e-0912
serous membrane7.26e-0912
intraembryonic coelom7.26e-0912
pharyngeal epithelium4.19e-086
gastrointestinal system5.00e-0725
Disease
Ontology termp-valuen
lymphoma1.16e-2710
genetic disease7.03e-131
monogenic disease7.03e-131
xeroderma pigmentosum7.03e-131
anemia1.57e-121
acute leukemia3.08e-121
lymphatic system cancer3.45e-121
lymphosarcoma3.45e-121
hematologic cancer1.91e-0751
immune system cancer1.91e-0751
hematopoietic system disease6.80e-072


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)
MA0003.19.50746e-05
MA0004.10.080382
MA0006.10.107826
MA0007.10.0722718
MA0009.10.385713
MA0014.10.000209122
MA0017.10.601639
MA0019.10.158371
MA0024.10.303271
MA0025.10.497679
MA0027.11.91867
MA0028.10.121511
MA0029.10.852369
MA0030.10.30925
MA0031.10.723388
MA0038.10.818715
MA0040.11.55443
MA0041.11.54033
MA0042.10.934037
MA0043.10.38597
MA0046.10.376892
MA0048.10.181863
MA0050.10.93692
MA0051.10.808446
MA0052.10.325534
MA0055.10.233188
MA0056.10
MA0057.10.0894026
MA0058.10.16729
MA0059.10.672433
MA0060.10.097271
MA0061.13.38674
MA0063.10
MA0066.10.413239
MA0067.10.661236
MA0068.10.192805
MA0069.10.373781
MA0070.10.364788
MA0071.10.358524
MA0072.10.361192
MA0073.11.02142e-06
MA0074.10.405541
MA0076.10.0488952
MA0077.10.934844
MA0078.10.554788
MA0081.10.672921
MA0083.11.0158
MA0084.10.834984
MA0087.10.359239
MA0088.10.182616
MA0089.10
MA0090.10.199262
MA0091.10.986582
MA0092.10.232971
MA0093.10.110354
MA0095.10
MA0098.10
MA0100.10.432601
MA0101.12.60341
MA0103.10.465544
MA0105.11.1776
MA0106.12.11396
MA0107.14.02458
MA0108.21.32368
MA0109.10
MA0111.10.21427
MA0113.10.961857
MA0114.10.791217
MA0115.10.592273
MA0116.10.550465
MA0117.10.416571
MA0119.10.346732
MA0122.10.438159
MA0124.10.555413
MA0125.11.21157
MA0130.10
MA0131.10.201414
MA0132.10
MA0133.10
MA0135.10.410584
MA0136.11.35254
MA0139.10.00305399
MA0140.10.719477
MA0141.10.667208
MA0142.10.670879
MA0143.10.497764
MA0144.11.77852
MA0145.10.137416
MA0146.10.0435096
MA0147.10.0133837
MA0148.12.78817
MA0149.10.696747
MA0062.20.671388
MA0035.20.109476
MA0039.26.34635e-06
MA0138.20.190328
MA0002.21.41406
MA0137.21.7091
MA0104.20.00601882
MA0047.22.75738
MA0112.20.60016
MA0065.20.67817
MA0150.10.428432
MA0151.10
MA0152.10.113254
MA0153.10.467885
MA0154.11.42564
MA0155.10.0568093
MA0156.11.27602
MA0157.10.626418
MA0158.10
MA0159.10.851576
MA0160.11.1121
MA0161.10
MA0162.15.79688e-05
MA0163.10.00250554
MA0164.10.173709
MA0080.21.16388
MA0018.20.156863
MA0099.20.364364
MA0079.28.99802e-11
MA0102.20.870137
MA0258.10.440052
MA0259.10.014781
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
BATF#1053875.166806440791680.000326241690494330.00332737850718138
BCL11A#5333576.017763203795440.0001283193637231140.00170568232504496
EBF1#1879256.747323368612889.95619081306104e-182.14837729819273e-15
IRF4#3662106.640761420225491.36753689995089e-065.32727289421748e-05
MEF2A#4205116.247743636548026.4050131274486e-072.90840506964176e-05
MEF2C#420878.76301458934451.19086481273547e-050.000301071726403486
NFKB1#4790243.991318853959151.22269380056977e-111.51659047313191e-09
PAX5#5079112.223188510392610.006749009079409910.0286831512673757
POLR2A#5430291.887155821823768.87752431645193e-073.82807498796831e-05
POU2F2#545292.483488379384320.007649629899002980.0315105978158071
SPI1#6688143.480622094524791.33337707023643e-050.00032551792388598
ZEB1#693594.605936004784699.33815167125314e-050.00135698792596912



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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