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{{Coexpression_clusters
{
|full_id=C218_tonsil_lymph_CD19_spleen_colon_appendix_salivary
|gostat_on_coexpression_clusters

Latest revision as of 10:58, 17 September 2013


Full id: C218_tonsil_lymph_CD19_spleen_colon_appendix_salivary



Phase1 CAGE Peaks

Hg19::chr14:106330824..106330846,-p1@IGHJ3
Hg19::chr14:106380481..106380483,-p@chr14:106380481..106380483
-
Hg19::chr14:106453155..106453176,-p1@IGHV1-2
Hg19::chr14:106471723..106471733,-p1@IGHV1-3
Hg19::chr14:106494587..106494603,-p1@IGHV2-5
Hg19::chr14:106512292..106512308,-p1@IGHV3-6
Hg19::chr14:106518922..106518940,-p1@IGHV3-7
Hg19::chr14:106539557..106539581,-p1@IGHV1-8
Hg19::chr14:106586656..106586668,-p1@IGHV3-13
Hg19::chr14:106668105..106668116,-p1@IGHV3-20
Hg19::chr14:106692191..106692211,-p1@IGHV3-21
Hg19::chr14:106725723..106725742,-p1@IGHV3-23
Hg19::chr14:106733624..106733650,-p1@IGHV1-24
Hg19::chr14:106746150..106746153,-p1@IGHV3-25
Hg19::chr14:106845840..106845851,-p1@IGHV3-35
Hg19::chr14:106967526..106967551,-p1@IGHV1-46
Hg19::chr14:106994333..106994352,-p1@IGHV3-48
Hg19::chr14:107013453..107013460,-p2@IGHV3-49
Hg19::chr14:107013465..107013481,-p1@IGHV3-49
Hg19::chr14:107035208..107035226,-p1@IGHV5-51
Hg19::chr14:107035284..107035314,-p2@IGHV5-51
Hg19::chr14:107078851..107078874,-p1@IGHV1-58
Hg19::chr14:107083690..107083722,-p1@IGHV4-59
Hg19::chr14:107099659..107099670,-p1@IGHV3-62
Hg19::chr14:107179265..107179287,-p1@IGHV2-70
Hg19::chr14:107183929..107183940,-p1@IGHV3-71
Hg19::chr14:107199464..107199472,-p1@IGHV3-72
Hg19::chr14:107211459..107211478,-p1@IGHV3-73
Hg19::chr14:107259809..107259829,-p1@uc001yta.1
Hg19::chr14:107281429..107281433,-p1@IGHV4-80
Hg19::chr19:42381173..42381198,+p2@CD79A
Hg19::chr22:17403095..17403096,-p1@IGKV2OR22-3
Hg19::chr22:22516550..22516571,+p1@IGLV4-60
Hg19::chr22:22677237..22677284,+p1@AY998676
Hg19::chr22:22681656..22681657,+p1@IGLV1-50
Hg19::chr22:22712089..22712103,+p1@IGLV1-47
Hg19::chr22:22723969..22723985,+p1@IGLV7-46
Hg19::chr22:22730353..22730360,+p1@IGLV5-45
Hg19::chr22:22735194..22735208,+p1@IGLV1-44
Hg19::chr22:22749343..22749360,+p1@IGLV7-43
Hg19::chr22:22764088..22764105,+p1@IGLV1-40
Hg19::chr22:22764110..22764121,+p2@IGLV1-40
Hg19::chr22:22781853..22781858,+p1@IGLV5-37
Hg19::chr22:22786288..22786295,+p1@IGLV1-36
Hg19::chr22:22922260..22922267,+p1@IGLV2-34
Hg19::chr22:23006897..23006908,+p1@ENST00000385099
Hg19::chr22:23010756..23010763,+p1@IGLV3-27
Hg19::chr22:23029172..23029186,+p2@IGLV3-25
Hg19::chr22:23029188..23029205,+p1@IGLV3-25
Hg19::chr22:23063100..23063117,+p1@IGLV3-19
Hg19::chr22:23077065..23077071,+p1@IGLV2-18
Hg19::chr22:23114284..23114291,+p1@IGLV3-12
Hg19::chr22:23134974..23134990,+p1@IGLV2-11
Hg19::chr22:23154239..23154246,+p1@IGLV3-10
Hg19::chr22:23161576..23161592,+p1@IGLV3-9
Hg19::chr22:23165272..23165278,+p1@MIR650
Hg19::chr22:23222894..23222909,+p1@IGLV3-1
Hg19::chr22:23227695..23227702,-p@chr22:23227695..23227702
-
Hg19::chr22:23227835..23227842,+p@chr22:23227835..23227842
+
Hg19::chr22:23237558..23237573,+p@chr22:23237558..23237573
+
Hg19::chr2:114163945..114163953,+p1@ENST00000453673
Hg19::chr2:89185050..89185069,+p1@uc002stl.2
Hg19::chr2:89247338..89247342,-p1@IGKV1-5
Hg19::chr2:89278535..89278547,-p1@IGKV3-7
Hg19::chr2:89399845..89399854,-p1@IGKV1-16
Hg19::chr2:89513402..89513412,-p1@IGKV1-27
Hg19::chr2:89890533..89890539,+p1@uc010yts.1
Hg19::chr2:95637982..95637984,-p1@ENST00000429316


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

p.valueFDRnGenesnPathwayName
2.72719518243547e-178.63157275240828e-1517511Signaling in Immune system (Reactome):REACT_6900
4.06974933269274e-282.57615132759451e-251448{FCGR2B,50} (Static Module):NA



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:0003823antigen binding4.21115196817957e-05
GO:0006955immune response5.67426408314668e-05
GO:0002376immune system process6.98965686274625e-05
GO:0019815B cell receptor complex0.00536865337511534
GO:0019814immunoglobulin complex0.00536865337511534
GO:0005771multivesicular body0.00596490702026829
GO:0050853B cell receptor signaling pathway0.0140557926159866
GO:0001772immunological synapse0.0178836616630865
GO:0042100B cell proliferation0.0178836616630865
GO:0050851antigen receptor-mediated signaling pathway0.0196590009575182
GO:0030183B cell differentiation0.0196590009575182
GO:0002429immune response-activating cell surface receptor signaling pathway0.0196590009575182
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0196590009575182
GO:0002757immune response-activating signal transduction0.0196590009575182
GO:0002764immune response-regulating signal transduction0.0196590009575182
GO:0045121lipid raft0.023659252672592
GO:0009897external side of plasma membrane0.023659252672592
GO:0005770late endosome0.023659252672592
GO:0032943mononuclear cell proliferation0.023659252672592
GO:0046651lymphocyte proliferation0.023659252672592
GO:0042113B cell activation0.0259246100408165
GO:0030098lymphocyte differentiation0.0259598057034707
GO:0002253activation of immune response0.0275385060338675
GO:0050778positive regulation of immune response0.0306676533211757
GO:0002684positive regulation of immune system process0.0306676533211757
GO:0002521leukocyte differentiation0.0308542166241833
GO:0050776regulation of immune response0.0318196556640933
GO:0002682regulation of immune system process0.0318196556640933
GO:0051240positive regulation of multicellular organismal process0.0322514226524992
GO:0043235receptor complex0.0326537506581756
GO:0009986cell surface0.0424455817755085
GO:0046649lymphocyte activation0.043050663867282
GO:0030097hemopoiesis0.0433505808108114
GO:0048534hemopoietic or lymphoid organ development0.0448795842241041
GO:0045321leukocyte activation0.0448795842241041
GO:0002520immune system development0.0448795842241041
GO:0005768endosome0.0462833074571253
GO:0001775cell activation0.0487668118354535



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
B cell3.14e-2314
lymphocyte of B lineage2.13e-1224
pro-B cell2.13e-1224
single nucleate cell7.79e-083
mononuclear cell7.79e-083
Uber Anatomy
Ontology termp-valuen
adult organism1.38e-51114
blood3.85e-2215
haemolymphatic fluid3.85e-2215
organism substance3.85e-2215


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)
MA0003.12.59252e-10
MA0004.10.149722
MA0006.10.00118131
MA0007.10.267938
MA0009.10.177487
MA0014.16.78641e-09
MA0017.10.801103
MA0019.10.355082
MA0024.10.120483
MA0025.10.263258
MA0027.11.60746
MA0028.10.00158283
MA0029.10.810474
MA0030.10.1244
MA0031.10.094053
MA0038.10.524788
MA0040.10.133239
MA0041.10.0136316
MA0042.10.0490749
MA0043.10.177674
MA0046.10.171104
MA0048.12.1057
MA0050.10.0494713
MA0051.10.0275428
MA0052.10.420641
MA0055.10.141835
MA0056.10
MA0057.10.0472222
MA0058.10.147592
MA0059.10.0201958
MA0060.16.50359e-05
MA0061.10.56081
MA0063.10
MA0066.10.525815
MA0067.10.400371
MA0068.10.238262
MA0069.10.168868
MA0070.10.162448
MA0071.10.0913056
MA0072.10.159899
MA0073.10.000118303
MA0074.10.512862
MA0076.10.00432033
MA0077.10.155571
MA0078.11.17809
MA0081.10.0640981
MA0083.10.181949
MA0084.10.555931
MA0087.10.15852
MA0088.10.00599891
MA0089.10
MA0090.10.190895
MA0091.10.307525
MA0092.10.00761758
MA0093.10.15826
MA0095.10
MA0098.10
MA0100.10.304845
MA0101.10.879595
MA0103.13.2286
MA0105.10.274012
MA0106.10.038444
MA0107.10.493578
MA0108.20.639445
MA0109.10
MA0111.10.212067
MA0113.10.165308
MA0114.10.322312
MA0115.10.90409
MA0116.10.227474
MA0117.10.200286
MA0119.10.0164259
MA0122.10.216641
MA0124.10.310325
MA0125.10.251003
MA0130.10
MA0131.10.0603216
MA0132.10
MA0133.10
MA0135.11.0819
MA0136.10.294339
MA0139.11.24496
MA0140.11.03138
MA0141.10.268319
MA0142.12.01176
MA0143.10.165465
MA0144.10.020336
MA0145.10.0101852
MA0146.10.128343
MA0147.10.0111897
MA0148.10.178324
MA0149.10.0186085
MA0062.20.000227345
MA0035.21.0284
MA0039.20.00629893
MA0138.21.65869
MA0002.20.857304
MA0137.20.0400708
MA0104.20.000624228
MA0047.20.14099
MA0112.21.40155
MA0065.21.02053
MA0150.11.06276
MA0151.10
MA0152.10.720736
MA0153.10.239658
MA0154.10.455264
MA0155.10.651567
MA0156.10.100014
MA0157.10.0700329
MA0158.10
MA0159.12.14457
MA0160.10.0766811
MA0161.10
MA0162.11.21106e-09
MA0163.15.93858e-05
MA0164.10.0465359
MA0080.20.0310499
MA0018.20.0388114
MA0099.20.0940879
MA0079.26.55743e-15
MA0102.20.588272
MA0258.11.69749
MA0259.10.00317815
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
POU2F2#5452182.410444603520080.0002979316629091410.00307771364417089



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

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