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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.141425727858451

Latest revision as of 11:49, 17 September 2013


Full id: C1680_Neutrophils_Eosinophils_pineal_optic_cerebellum_pituitary_parietal



Phase1 CAGE Peaks

Hg19::chr12:62860581..62860620,+p1@MON2
Hg19::chr1:12290063..12290118,+p1@VPS13D
Hg19::chr4:123073464..123073547,+p1@KIAA1109
Hg19::chr6:38607673..38607749,-p1@BTBD9
Hg19::chr8:9413410..9413451,+p1@TNKS


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:0008104protein localization0.0113683186556758
GO:0033036macromolecule localization0.0113683186556758
GO:0018107peptidyl-threonine phosphorylation0.0113683186556758
GO:0018210peptidyl-threonine modification0.0113683186556758
GO:0006895Golgi to endosome transport0.0170257968800675
GO:0000139Golgi membrane0.0170257968800675
GO:0018209peptidyl-serine modification0.0170257968800675
GO:0018105peptidyl-serine phosphorylation0.0170257968800675
GO:0044431Golgi apparatus part0.0170257968800675
GO:0007004telomere maintenance via telomerase0.0257469581026292
GO:0006892post-Golgi vesicle-mediated transport0.0289068878369803
GO:0005794Golgi apparatus0.0312744347931803
GO:0032200telomere organization and biogenesis0.0312744347931803
GO:0000723telomere maintenance0.0312744347931803
GO:0000781chromosome, telomeric region0.0312744347931803
GO:0003950NAD+ ADP-ribosyltransferase activity0.0352887257354325
GO:0016197endosome transport0.0352887257354325
GO:0015031protein transport0.0352887257354325
GO:0046907intracellular transport0.035882627027328
GO:0045184establishment of protein localization0.035882627027328
GO:0012505endomembrane system0.0408007570046309
GO:0006278RNA-dependent DNA replication0.0408007570046309
GO:0051649establishment of cellular localization0.0408007570046309
GO:0065002intracellular protein transport across a membrane0.0408007570046309
GO:0051641cellular localization0.0408007570046309
GO:0016763transferase activity, transferring pentosyl groups0.0408007570046309
GO:0051028mRNA transport0.0408007570046309
GO:0004190aspartic-type endopeptidase activity0.0408007570046309
GO:0005643nuclear pore0.0408007570046309
GO:0048193Golgi vesicle transport0.0408007570046309
GO:0050658RNA transport0.0408007570046309
GO:0051236establishment of RNA localization0.0408007570046309
GO:0050657nucleic acid transport0.0408007570046309
GO:0006403RNA localization0.0408007570046309
GO:0046930pore complex0.0417767984157967
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0435294639387703
GO:0044453nuclear membrane part0.0451850483065894
GO:0018193peptidyl-amino acid modification0.0477275083872672
GO:0031090organelle membrane0.0477275083872672
GO:0051179localization0.0479964255474786



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>

Uber Anatomy
Ontology termp-valuen
adult organism6.43e-44114
neural tube9.72e-2756
neural rod9.72e-2756
future spinal cord9.72e-2756
neural keel9.72e-2756
regional part of nervous system5.13e-2553
regional part of brain5.13e-2553
regional part of forebrain2.15e-2341
forebrain2.15e-2341
anterior neural tube2.15e-2341
future forebrain2.15e-2341
central nervous system1.24e-2281
brain1.30e-2268
future brain1.30e-2268
nervous system3.11e-2289
brain grey matter2.05e-1934
gray matter2.05e-1934
telencephalon2.59e-1934
regional part of telencephalon3.20e-1832
cerebral hemisphere4.07e-1832
neurectoderm4.86e-1686
neural plate8.83e-1682
presumptive neural plate8.83e-1682
regional part of cerebral cortex5.58e-1522
cerebral cortex3.58e-1425
pallium3.58e-1425
neocortex1.07e-1320
pre-chordal neural plate1.55e-1261
ectoderm-derived structure8.12e-10171
ectoderm8.12e-10171
presumptive ectoderm8.12e-10171
ecto-epithelium1.43e-09104
structure with developmental contribution from neural crest2.81e-09132
hematopoietic system6.09e-0898
blood island6.09e-0898
organ system subdivision4.86e-07223
hemolymphoid system6.47e-07108
basal ganglion8.27e-079
nuclear complex of neuraxis8.27e-079
aggregate regional part of brain8.27e-079
collection of basal ganglia8.27e-079
cerebral subcortex8.27e-079
neural nucleus9.78e-079
nucleus of brain9.78e-079


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)
MA0003.11.80249
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.02528
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.11.55172
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.215829
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.11.76306
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.21.41923
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.839774
MA0065.20.449243
MA0150.11.35623
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.409315
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.11.05321
MA0164.10.810347
MA0080.20.456437
MA0018.21.83842
MA0099.20.699641
MA0079.21.03616
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
CCNT2#90545.068961261570110.002709998091280770.0148915863756326
E2F1#186943.925911371903460.007214984547106360.0298698129430864
E2F6#187655.017155731697390.0003144978599297790.00322555651509439
ELF1#199754.258097958807540.0007142416939776840.00572747913677329
HEY1#2346254.040111043105710.0009288852205177990.00673740145466063
IRF1#365946.109731002851120.001315525264767990.00880775326156192
MXI1#460135.976942977255580.008653004889366880.0329460874094272
NANOG#79923211.69791139240510.01091164951956080.0402160343075629
NFKB1#479055.488063424193840.0002008162847462320.00238845825789906
SIN3A#2594255.408884726815140.0002159522671657270.00247844382752982
SIX5#147912413.66937228436725.58844770365977e-050.0009374428039231
SRF#6722411.03774260973420.0001299255814846750.00171005643411191
TAF1#687253.343046285745290.002394600090870310.0135220134571724
THAP1#55145212.54765784114050.009528434667386530.0358893605102128



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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