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Coexpression cluster:C1600: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1600_blood_Whole_optic_spinal_locus_globus_thalamus
|gostat_on_coexpression_clusters=GO:0005813!centrosome!0.00275378218751093!84333;3796$GO:0005815!microtubule organizing center!0.00275378218751093!84333;3796$GO:0015630!microtubule cytoskeleton!0.0226534454319709!84333;3796
|id=C1600
|ontology_enrichment_celltype=CL:0000838!2.03e-09!52;CL:0000542!4.39e-09!53;CL:0000051!4.39e-09!53
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.44e-50!115;UBERON:0001049!5.36e-26!57;UBERON:0005068!5.36e-26!57;UBERON:0006241!5.36e-26!57;UBERON:0007135!5.36e-26!57;UBERON:0003080!3.60e-22!42;UBERON:0002780!1.07e-21!41;UBERON:0001890!1.07e-21!41;UBERON:0006240!1.07e-21!41;UBERON:0001017!9.47e-21!82;UBERON:0002616!3.98e-20!59;UBERON:0000073!1.02e-19!94;UBERON:0001016!1.02e-19!94;UBERON:0000955!1.68e-19!69;UBERON:0006238!1.68e-19!69;UBERON:0005743!3.02e-19!86;UBERON:0002020!3.90e-18!34;UBERON:0003528!3.90e-18!34;UBERON:0001893!6.18e-18!34;UBERON:0002791!1.83e-17!33;UBERON:0001869!1.01e-16!32;UBERON:0003075!1.48e-14!86;UBERON:0007284!1.48e-14!86;UBERON:0002619!5.27e-14!22;UBERON:0002346!2.19e-13!90;UBERON:0000956!7.00e-13!25;UBERON:0000203!7.00e-13!25;UBERON:0001950!8.82e-13!20;UBERON:0000153!1.02e-11!129;UBERON:0007811!1.02e-11!129;UBERON:0003056!2.35e-11!61;UBERON:0000033!3.36e-10!123;UBERON:0004121!1.17e-08!169;UBERON:0000178!2.90e-08!15;UBERON:0000179!2.90e-08!15;UBERON:0000463!2.90e-08!15;UBERON:0000924!3.73e-08!173;UBERON:0006601!3.73e-08!173;UBERON:0002308!8.43e-07!9;UBERON:0000125!8.43e-07!9
}}

Latest revision as of 11:48, 17 September 2013


Full id: C1600_blood_Whole_optic_spinal_locus_globus_thalamus



Phase1 CAGE Peaks

Hg19::chr10:92922581..92922624,+p5@PCGF5
Hg19::chr10:92922625..92922667,+p6@PCGF5
Hg19::chr12:861717..861770,+p1@WNK1
Hg19::chr5:61602025..61602053,+p2@KIF2A
Hg19::chr5:61602055..61602083,+p3@KIF2A


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:0005813centrosome0.00275378218751093
GO:0005815microtubule organizing center0.00275378218751093
GO:0015630microtubule cytoskeleton0.0226534454319709



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
lymphoid lineage restricted progenitor cell9.56e-0752
Uber Anatomy
Ontology termp-valuen
adult organism5.89e-47114
neural tube2.24e-2556
neural rod2.24e-2556
future spinal cord2.24e-2556
neural keel2.24e-2556
regional part of nervous system1.46e-2353
regional part of brain1.46e-2353
regional part of forebrain6.41e-2141
forebrain6.41e-2141
anterior neural tube6.41e-2141
future forebrain6.41e-2141
central nervous system1.55e-2081
nervous system5.91e-2089
brain1.78e-1868
future brain1.78e-1868
brain grey matter1.91e-1734
gray matter1.91e-1734
telencephalon3.24e-1734
regional part of telencephalon3.32e-1632
cerebral hemisphere4.77e-1632
neural plate1.05e-1482
presumptive neural plate1.05e-1482
neurectoderm8.19e-1486
regional part of cerebral cortex9.59e-1422
neocortex1.61e-1220
cerebral cortex2.92e-1225
pallium2.92e-1225
pre-chordal neural plate9.00e-1161
organ system subdivision5.84e-09223
ecto-epithelium1.17e-08104
blood2.96e-0815
haemolymphatic fluid2.96e-0815
organism substance2.96e-0815
ectoderm-derived structure6.23e-08171
ectoderm6.23e-08171
presumptive ectoderm6.23e-08171
structure with developmental contribution from neural crest3.72e-07132
neural nucleus9.35e-079
nucleus of brain9.35e-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)
MA0003.111.4791
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.45664
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.12.1751
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.860776
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.12.48388
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.12.58868
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
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
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
MA0139.12.13391
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.442008
MA0146.15.56258
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.527987
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.14.22787
MA0163.10.168633
MA0164.11.89806
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.54347
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
ATF3#467313.47790471560530.0008241088551409360.00627234402580267
BCLAF1#9774312.99158856607310.0009178032402542550.00667510115660962
CHD2#110636.206413700470110.007774550126275590.0319445369674284
E2F1#186954.907389214879320.0003512818099256460.00352121325912511
EGR1#195854.988179094810140.0003237398000590710.00330315171730845
ETS1#211335.83725655332140.009253279045631430.0349639366948879
HDAC8#558692310.6336134453781.6469764092501e-050.000380129434708667
NANOG#79923317.54686708860760.0003794200090681830.00375960591338443
NRF1#489937.326167668626540.004839689817117540.0226843355538075
POU2F2#545235.463674434645510.01115650094469780.040998374460355
SETDB1#9869216.12801047120420.00585057846659340.0262672411861641
SIN3A#2594255.408884726815140.0002159522671657270.00247762702741089
STAT2#6773226.10550847457630.002275903944310060.0129209138964883
TFAP2C#702248.647382887888180.0003390518878174050.00344792990377429



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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