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Coexpression cluster:C1130: Difference between revisions

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{{Coexpression_clusters
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telomeric DNA binding!0.0250906422742618!5813$GO:0005662!DNA replication factor A complex!0.0250906422742618!5813$GO:0000784!nuclear chromosome, telomeric region!0.0250906422742618!5813$GO:0043601!nuclear replisome!0.0250906422742618!5813$GO:0030894!replisome!0.0250906422742618!5813$GO:0000145!exocyst!0.0250906422742618!23233$GO:0042162!telomeric DNA binding!0.0250906422742618!5813$GO:0046332!SMAD binding!0.0250906422742618!5813$GO:0006268!DNA unwinding during replication!0.0250906422742618!5813$GO:0043596!nuclear replication fork!0.0250906422742618!5813$GO:0032392!DNA geometric change!0.0250906422742618!5813$GO:0032508!DNA duplex unwinding!0.0250906422742618!5813$GO:0016998!cell wall catabolic process!0.0250906422742618!135112$GO:0010382!cell wall metabolic process!0.0250906422742618!135112$GO:0007047!cell wall organization and biogenesis!0.0250906422742618!135112$GO:0045229!external encapsulating structure organization and biogenesis!0.025871678251679!135112$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.0298750678121566!5813$GO:0000781!chromosome, telomeric region!0.0310576474269521!5813$GO:0005657!replication fork!0.0310576474269521!5813$GO:0006904!vesicle docking during exocytosis!0.0310576474269521!23233$GO:0006270!DNA replication initiation!0.0310576474269521!5813$GO:0048278!vesicle docking!0.0310576474269521!23233$GO:0022406!membrane docking!0.0310576474269521!23233$GO:0044448!cell cortex part!0.0352318202835125!23233$GO:0003697!single-stranded DNA binding!0.0458051730286997!5813$GO:0005938!cell cortex!0.0462013451222497!23233$GO:0044454!nuclear chromosome 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5119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;2.22341,MA0138.2;0.704862,MA0002.2;0.611548,MA0137.2;0.36398,MA0104.2;0.636673,MA0047.2;0.636643,MA0112.2;0.0758925,MA0065.2;0.996317,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.335384,MA0155.1;0.910701,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;2.01861,MA0163.1;0.632664,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;6.42888,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0}}
|full_id=C1130_optic_globus_thalamus_spinal_occipital_locus_pons
|id=C1130
}}

Latest revision as of 11:38, 17 September 2013


Full id: C1130_optic_globus_thalamus_spinal_occipital_locus_pons



Phase1 CAGE Peaks

Hg19::chr11:111848024..111848087,+p1@DIXDC1
Hg19::chr1:78245303..78245351,+p1@FAM73A
Hg19::chr20:16554078..16554113,-p2@KIF16B
Hg19::chr2:73053126..73053184,-p1@EXOC6B
Hg19::chr5:139487363..139487444,+p1@PURA
Hg19::chr5:139487608..139487663,+p3@PURA
Hg19::chr6:126112074..126112144,+p1@NCOA7


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:0003691double-stranded telomeric DNA binding0.0250906422742618
GO:0005662DNA replication factor A complex0.0250906422742618
GO:0000784nuclear chromosome, telomeric region0.0250906422742618
GO:0043601nuclear replisome0.0250906422742618
GO:0030894replisome0.0250906422742618
GO:0000145exocyst0.0250906422742618
GO:0042162telomeric DNA binding0.0250906422742618
GO:0046332SMAD binding0.0250906422742618
GO:0006268DNA unwinding during replication0.0250906422742618
GO:0043596nuclear replication fork0.0250906422742618
GO:0032392DNA geometric change0.0250906422742618
GO:0032508DNA duplex unwinding0.0250906422742618
GO:0016998cell wall catabolic process0.0250906422742618
GO:0010382cell wall metabolic process0.0250906422742618
GO:0007047cell wall organization and biogenesis0.0250906422742618
GO:0045229external encapsulating structure organization and biogenesis0.025871678251679
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0298750678121566
GO:0000781chromosome, telomeric region0.0310576474269521
GO:0005657replication fork0.0310576474269521
GO:0006904vesicle docking during exocytosis0.0310576474269521
GO:0006270DNA replication initiation0.0310576474269521
GO:0048278vesicle docking0.0310576474269521
GO:0022406membrane docking0.0310576474269521
GO:0044448cell cortex part0.0352318202835125
GO:0003697single-stranded DNA binding0.0458051730286997
GO:0005938cell cortex0.0462013451222497
GO:0044454nuclear chromosome part0.0465674358244908



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.17e-44114
neural tube2.75e-2556
neural rod2.75e-2556
future spinal cord2.75e-2556
neural keel2.75e-2556
regional part of nervous system1.66e-2353
regional part of brain1.66e-2353
brain6.97e-2268
future brain6.97e-2268
regional part of forebrain1.79e-2141
forebrain1.79e-2141
anterior neural tube1.79e-2141
future forebrain1.79e-2141
central nervous system9.34e-2081
nervous system5.83e-1989
brain grey matter1.51e-1734
gray matter1.51e-1734
telencephalon1.52e-1734
neural plate5.89e-1782
presumptive neural plate5.89e-1782
neurectoderm7.99e-1786
structure with developmental contribution from neural crest2.35e-16132
cerebral hemisphere2.57e-1632
regional part of telencephalon2.67e-1632
regional part of cerebral cortex2.33e-1422
neocortex4.04e-1320
ectoderm-derived structure4.89e-12171
ectoderm4.89e-12171
presumptive ectoderm4.89e-12171
cerebral cortex5.74e-1225
pallium5.74e-1225
pre-chordal neural plate5.87e-1261
organ system subdivision1.96e-10223
ecto-epithelium3.00e-10104
anatomical conduit2.41e-08240
multi-tissue structure7.20e-08342
anatomical cluster1.26e-07373
neural nucleus3.12e-079
nucleus of brain3.12e-079
basal ganglion3.22e-079
nuclear complex of neuraxis3.22e-079
aggregate regional part of brain3.22e-079
collection of basal ganglia3.22e-079
cerebral subcortex3.22e-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)
MA0003.11.35295
MA0004.10.502801
MA0006.11.62096
MA0007.10.483857
MA0009.10.973289
MA0014.12.12603
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.940207
MA0029.10.886702
MA0030.10.875089
MA0031.11.8966
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.744639
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.11.70839
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.11.11391
MA0091.10.505453
MA0092.11.17914
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.11.68581
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.11.46178
MA0146.10.828373
MA0147.10.768766
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.22.22341
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.636673
MA0047.20.636643
MA0112.20.0758925
MA0065.20.996317
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.910701
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.12.01861
MA0163.10.632664
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.26.42888
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
EGR1#195853.562985067721530.004722351211058930.0222572154940107
ELF1#199763.649798250406460.0009377479782620690.0067884841686915
HEY1#2346263.462952322662040.001267890095872120.00850408925070894
HMGN3#932444.673455841914620.005751881099938870.0259054168009192
MYC#460953.730201336863860.003821944222306690.0188674623101479
NR2C2#7182313.97769038796040.000918991307240130.00668234582864666
PAX5#507943.811180303530190.01208261681555190.0438234560722147
POLR2A#543072.147453176558070.004747636447610280.0223250068866263
TAF1#687262.865468244924540.003728330207471460.0185827564445028



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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