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Coexpression cluster:C157: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 10:45, 17 September 2013


Full id: C157_testicular_H9_testis_iPS_teratocarcinoma_colon_trachea



Phase1 CAGE Peaks

Hg19::chr10:135043493..135043510,+p2@UTF1
Hg19::chr10:135043674..135043682,+p9@UTF1
Hg19::chr10:135043690..135043701,+p4@UTF1
Hg19::chr10:135044076..135044090,+p8@UTF1
Hg19::chr10:135044170..135044188,+p7@UTF1
Hg19::chr10:135051353..135051367,+p1@VENTX
Hg19::chr10:98072001..98072012,-p@chr10:98072001..98072012
-
Hg19::chr10:98497275..98497286,+p@chr10:98497275..98497286
+
Hg19::chr11:118842467..118842477,+p1@FOXR1
Hg19::chr11:64136967..64136975,+p@chr11:64136967..64136975
+
Hg19::chr12:102133233..102133245,-p1@SYCP3
Hg19::chr12:31804934..31804953,-p@chr12:31804934..31804953
-
Hg19::chr12:31804958..31804974,-p@chr12:31804958..31804974
-
Hg19::chr12:4130254..4130285,+p@chr12:4130254..4130285
+
Hg19::chr12:7843093..7843102,-p@chr12:7843093..7843102
-
Hg19::chr12:7843145..7843150,-p@chr12:7843145..7843150
-
Hg19::chr12:7843168..7843173,-p@chr12:7843168..7843173
-
Hg19::chr12:7848349..7848359,-p2@GDF3
Hg19::chr12:7848364..7848378,-p1@GDF3
Hg19::chr12:7848400..7848403,-p3@GDF3
Hg19::chr12:7904213..7904218,-p2@CLEC4C
Hg19::chr12:7954930..7954932,+p@chr12:7954930..7954932
+
Hg19::chr12:8045030..8045044,+p5@NANOGP1
Hg19::chr12:8983864..8983875,-p2@A2ML1-AS1
Hg19::chr13:25254545..25254550,+p1@ATP12A
Hg19::chr13:25254693..25254710,+p2@ATP12A
Hg19::chr14:51360992..51360997,+p@chr14:51360992..51360997
+
Hg19::chr14:53299036..53299048,+p@chr14:53299036..53299048
+
Hg19::chr14:96152791..96152796,+p2@TCL1B
Hg19::chr14:99604394..99604433,-p@chr14:99604394..99604433
-
Hg19::chr15:35306088..35306093,+p@chr15:35306088..35306093
+
Hg19::chr15:89665804..89665808,-p@chr15:89665804..89665808
-
Hg19::chr15:98937858..98937881,-p@chr15:98937858..98937881
-
Hg19::chr16:24506492..24506513,-p1@BX538205
Hg19::chr16:70484243..70484248,-p@chr16:70484243..70484248
-
Hg19::chr16:71475936..71475963,-p@chr16:71475936..71475963
-
Hg19::chr16:9277969..9277994,+p@chr16:9277969..9277994
+
Hg19::chr17:19395753..19395759,+p@chr17:19395753..19395759
+
Hg19::chr19:13297435..13297437,+p@chr19:13297435..13297437
+
Hg19::chr19:42811002..42811015,+p@chr19:42811002..42811015
+
Hg19::chr19:46003039..46003051,+p6@PPM1N
Hg19::chr19:46003056..46003067,+p11@PPM1N
Hg19::chr19:46236688..46236701,+p1@ENST00000457052
Hg19::chr19:51883856..51883866,-p@chr19:51883856..51883866
-
Hg19::chr19:51883879..51883908,-p@chr19:51883879..51883908
-
Hg19::chr19:51883915..51883934,-p@chr19:51883915..51883934
-
Hg19::chr19:51883942..51883949,-p@chr19:51883942..51883949
-
Hg19::chr19:54168219..54168226,+p@chr19:54168219..54168226
+
Hg19::chr19:54290224..54290230,+p@chr19:54290224..54290230
+
Hg19::chr19:54290483..54290487,+p1@MIR371A
Hg19::chr19:55976108..55976119,-p@chr19:55976108..55976119
-
Hg19::chr1:155804359..155804366,-p@chr1:155804359..155804366
-
Hg19::chr1:155804376..155804383,-p@chr1:155804376..155804383
-
Hg19::chr1:155804425..155804436,-p@chr1:155804425..155804436
-
Hg19::chr1:156152062..156152074,+p@chr1:156152062..156152074
+
Hg19::chr1:200004156..200004159,+p@chr1:200004156..200004159
+
Hg19::chr1:200008057..200008103,+p1@BC080182
Hg19::chr1:65612630..65612670,+p@chr1:65612630..65612670
+
Hg19::chr1:92414952..92414965,+p1@BRDT
Hg19::chr20:50419112..50419117,-p10@SALL4
Hg19::chr21:45765639..45765654,-p@chr21:45765639..45765654
-
Hg19::chr21:45766204..45766222,-p@chr21:45766204..45766222
-
Hg19::chr21:47831204..47831214,+p@chr21:47831204..47831214
+
Hg19::chr22:17092528..17092530,+p@chr22:17092528..17092530
+
Hg19::chr22:27024930..27024945,+p@chr22:27024930..27024945
+
Hg19::chr2:27038042..27038048,+p@chr2:27038042..27038048
+
Hg19::chr3:109033438..109033449,-p@chr3:109033438..109033449
-
Hg19::chr3:109056727..109056765,+p2@ENST00000508178
Hg19::chr3:109128905..109128913,+p2@FLJ25363
Hg19::chr3:109128961..109129009,+p1@ENST00000489670
Hg19::chr3:115824886..115824897,-p@chr3:115824886..115824897
-
Hg19::chr3:194118687..194118692,-p4@GP5
Hg19::chr3:32838056..32838060,-p@chr3:32838056..32838060
-
Hg19::chr3:39268574..39268596,+p@chr3:39268574..39268596
+
Hg19::chr4:113571600..113571617,+p@chr4:113571600..113571617
+
Hg19::chr4:155702419..155702437,+p1@RBM46
Hg19::chr4:189030755..189030765,-p1@TRIML2
Hg19::chr4:2764786..2764789,+p@chr4:2764786..2764789
+
Hg19::chr5:150377663..150377680,-p@chr5:150377663..150377680
-
Hg19::chr5:176558815..176558850,+p@chr5:176558815..176558850
+
Hg19::chr6:2962186..2962206,-p21@SERPINB6
Hg19::chr6:38891759..38891774,+p@chr6:38891759..38891774
+
Hg19::chr6:38891781..38891789,+p@chr6:38891781..38891789
+
Hg19::chr6:38891794..38891799,+p@chr6:38891794..38891799
+
Hg19::chr6:38891807..38891809,+p@chr6:38891807..38891809
+
Hg19::chr6:74063949..74063957,-p3@DPPA5
Hg19::chr6:74104521..74104528,+p4@DDX43
Hg19::chr6:74104542..74104559,+p1@DDX43
Hg19::chr7:100293592..100293613,+p@chr7:100293592..100293613
+
Hg19::chr7:23749767..23749792,+p3@STK31
Hg19::chr7:23749832..23749845,+p2@STK31
Hg19::chr7:5447185..5447197,-p23@TNRC18
Hg19::chr7:6866868..6866875,-p3@CCZ1B
p4@CCZ1
Hg19::chr8:30244723..30244749,+p18@RBPMS
Hg19::chr8:42571671..42571675,-p@chr8:42571671..42571675
-
Hg19::chr9:101058489..101058493,+p@chr9:101058489..101058493
+
Hg19::chr9:139912749..139912794,-p8@ABCA2
Hg19::chr9:23779367..23779378,-p11@ELAVL2
Hg19::chr9:90692746..90692751,-p@chr9:90692746..90692751
-
Hg19::chr9:97402366..97402395,-p5@FBP1
Hg19::chrX:100548047..100548058,-p3@TAF7L
Hg19::chrX:100548065..100548075,-p4@TAF7L
Hg19::chrX:102965881..102965902,+p2@TMEM31
Hg19::chrX:103019822..103019825,-p@chrX:103019822..103019825
-
Hg19::chrX:103021870..103021902,-p@chrX:103021870..103021902
-
Hg19::chrX:114524275..114524308,+p1@LUZP4
Hg19::chrX:132568824..132568851,+p@chrX:132568824..132568851
+
Hg19::chrX:40482675..40482695,+p1@LOC347411
Hg19::chrX:40482706..40482715,+p2@LOC347411
Hg19::chrX:40482725..40482733,+p3@LOC347411


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:0006355regulation of transcription, DNA-dependent0.0181646542156121
GO:0016070RNA metabolic process0.0181646542156121
GO:0006351transcription, DNA-dependent0.0181646542156121
GO:0032774RNA biosynthetic process0.0181646542156121
GO:0003723RNA binding0.0181646542156121
GO:0051177meiotic sister chromatid cohesion0.0181646542156121
GO:0035093spermatogenesis, exchange of chromosomal proteins0.0181646542156121
GO:0032377regulation of intracellular lipid transport0.0181646542156121
GO:0032380regulation of intracellular sterol transport0.0181646542156121
GO:0007066female meiosis sister chromatid cohesion0.0181646542156121
GO:0000705achiasmate meiosis I0.0181646542156121
GO:0032383regulation of intracellular cholesterol transport0.0181646542156121
GO:0045449regulation of transcription0.0181646542156121
GO:0003676nucleic acid binding0.0181646542156121
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0181646542156121
GO:0006350transcription0.0181646542156121
GO:0003702RNA polymerase II transcription factor activity0.0181646542156121
GO:0010468regulation of gene expression0.0181646542156121
GO:0031323regulation of cellular metabolic process0.0181646542156121
GO:0005889hydrogen:potassium-exchanging ATPase complex0.0181646542156121
GO:0000802transverse filament0.0181646542156121
GO:0042132fructose-bisphosphatase activity0.0181646542156121
GO:0032374regulation of cholesterol transport0.0181646542156121
GO:0032371regulation of sterol transport0.0181646542156121
GO:0045132meiotic chromosome segregation0.0181646542156121
GO:0032368regulation of lipid transport0.0181646542156121
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0192157860280854
GO:0019222regulation of metabolic process0.0214597361942113
GO:0008900hydrogen:potassium-exchanging ATPase activity0.0214597361942113
GO:0043486histone exchange0.0214597361942113
GO:0007141male meiosis I0.0214597361942113
GO:0035092sperm chromatin condensation0.0214597361942113
GO:0007143female meiosis0.0214597361942113
GO:0007289spermatid nuclear differentiation0.024839339906988
GO:0032365intracellular lipid transport0.024839339906988
GO:0032366intracellular sterol transport0.024839339906988
GO:0032367intracellular cholesterol transport0.024839339906988
GO:0000800lateral element0.024839339906988
GO:0010467gene expression0.0294286409682944
GO:0043044ATP-dependent chromatin remodeling0.034508356674653
GO:0007130synaptonemal complex assembly0.034508356674653
GO:0050794regulation of cellular process0.0366681540950559
GO:0065007biological regulation0.0366681540950559
GO:0007129synapsis0.0366681540950559
GO:0007140male meiosis0.0366681540950559
GO:0004331fructose-2,6-bisphosphate 2-phosphatase activity0.0401090432575329
GO:0003730mRNA 3'-UTR binding0.0401090432575329
GO:0019203carbohydrate phosphatase activity0.0419063281638503
GO:0007062sister chromatid cohesion0.0419063281638503
GO:0043190ATP-binding cassette (ABC) transporter complex0.0419063281638503
GO:0042623ATPase activity, coupled0.0419063281638503
GO:0043283biopolymer metabolic process0.0462109027419868



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
embryonic stem cell9.04e-705
germ line cell6.12e-517
germ cell6.12e-517
melanocyte1.05e-0910
melanoblast1.05e-0910
pigment cell3.44e-0714
Uber Anatomy
Ontology termp-valuen
testis1.16e-448
male reproductive organ1.17e-3211
gonad2.28e-1721
indifferent external genitalia2.28e-1721
indifferent gonad2.28e-1721
gonad primordium2.28e-1721
external genitalia1.33e-1622
male organism1.33e-1622
male reproductive system1.33e-1622
body cavity3.83e-0846
reproductive organ8.12e-0848
body cavity or lining1.16e-0749
body cavity precursor5.55e-0754
Disease
Ontology termp-valuen
germ cell and embryonal cancer2.76e-2522
germ cell cancer2.76e-2522


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)
MA0003.12.44207e-06
MA0004.13.81855
MA0006.10.313654
MA0007.11.26858
MA0009.11.46781
MA0014.13.75611e-06
MA0017.10.215716
MA0019.10.441564
MA0024.10.0462041
MA0025.10.438389
MA0027.11.40191
MA0028.10.372818
MA0029.10.192642
MA0030.10.408624
MA0031.12.22843
MA0038.11.07874
MA0040.10.438057
MA0041.10.307772
MA0042.10.133457
MA0043.10.0815038
MA0046.10.0771926
MA0048.10.328986
MA0050.10.0649983
MA0051.10.0820645
MA0052.10.0548
MA0055.10.119153
MA0056.10
MA0057.10.362424
MA0058.11.25199
MA0059.12.15182
MA0060.110.7025
MA0061.10.0649524
MA0063.10
MA0066.10.0854411
MA0067.10.252035
MA0068.10.530747
MA0069.10.262233
MA0070.10.911684
MA0071.10.0595777
MA0072.10.245907
MA0073.10.00382594
MA0074.10.179569
MA0076.10.209585
MA0077.10.877682
MA0078.10.571981
MA0081.10.0207521
MA0083.13.35487
MA0084.10.387643
MA0087.10.892292
MA0088.10.0191968
MA0089.10
MA0090.10.143648
MA0091.10.851011
MA0092.10.667619
MA0093.13.08474
MA0095.10
MA0098.10
MA0100.10.0956758
MA0101.10.144248
MA0103.10.71227
MA0105.10.0550814
MA0106.10.0419553
MA0107.10.190173
MA0108.23.33991
MA0109.10
MA0111.10.594096
MA0113.10.472955
MA0114.10.618299
MA0115.10.203203
MA0116.10.131506
MA0117.10.320096
MA0119.10.080436
MA0122.10.35056
MA0124.10.528203
MA0125.11.334
MA0130.10
MA0131.10.0747247
MA0132.10
MA0133.10
MA0135.10.311792
MA0136.10.196205
MA0139.10.0757319
MA0140.11.49967
MA0141.10.566498
MA0142.12.02943
MA0143.10.726943
MA0144.11.43835
MA0145.10.356233
MA0146.10.0486491
MA0147.11.53407
MA0148.10.497685
MA0149.10.00257642
MA0062.20.0335185
MA0035.21.16493
MA0039.22.85847
MA0138.20.575378
MA0002.20.00360269
MA0137.21.16062
MA0104.21.05167
MA0047.20.629544
MA0112.20.00962691
MA0065.21.64938
MA0150.10.0307473
MA0151.10
MA0152.11.20692
MA0153.10.124754
MA0154.10.189023
MA0155.10.371878
MA0156.10.108855
MA0157.12.34677
MA0158.10
MA0159.10.709603
MA0160.10.360797
MA0161.10
MA0162.10.0306223
MA0163.10.0190953
MA0164.10.505053
MA0080.20.0411053
MA0018.20.0424766
MA0099.20.0621168
MA0079.20.123362
MA0102.20.416822
MA0258.10.116534
MA0259.13.16223
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

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