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Coexpression cluster:C503: Difference between revisions

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{{Coexpression_clusters
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|full_id=C503_occipital_spinal_thalamus_locus_optic_globus_pineal
|id=C503
|ontology_enrichment_celltype=CL:0000055!1.10e-12!180;CL:0000133!1.17e-07!59
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!4.55e-42!94;UBERON:0001016!4.55e-42!94;UBERON:0005743!4.01e-39!86;UBERON:0001017!6.58e-39!82;UBERON:0007023!3.80e-36!115;UBERON:0000924!5.10e-34!173;UBERON:0006601!5.10e-34!173;UBERON:0001049!7.51e-34!57;UBERON:0005068!7.51e-34!57;UBERON:0006241!7.51e-34!57;UBERON:0007135!7.51e-34!57;UBERON:0002346!1.13e-33!90;UBERON:0000955!2.51e-33!69;UBERON:0006238!2.51e-33!69;UBERON:0004121!7.41e-33!169;UBERON:0003075!1.14e-32!86;UBERON:0007284!1.14e-32!86;UBERON:0002616!2.52e-32!59;UBERON:0000033!8.72e-27!123;UBERON:0003080!2.21e-26!42;UBERON:0000153!3.57e-26!129;UBERON:0007811!3.57e-26!129;UBERON:0002780!5.08e-26!41;UBERON:0001890!5.08e-26!41;UBERON:0006240!5.08e-26!41;UBERON:0003056!2.59e-24!61;UBERON:0000475!1.20e-22!365;UBERON:0002020!1.06e-21!34;UBERON:0003528!1.06e-21!34;UBERON:0001893!1.57e-21!34;UBERON:0002791!5.91e-21!33;UBERON:0001869!2.25e-20!32;UBERON:0000468!5.77e-18!659;UBERON:0000956!4.50e-16!25;UBERON:0000203!4.50e-16!25;UBERON:0002619!1.84e-15!22;UBERON:0001950!3.59e-14!20;UBERON:0000481!2.12e-13!347;UBERON:0000467!3.05e-12!625;UBERON:0000922!3.52e-12!612;UBERON:0000480!6.42e-12!626;UBERON:0000119!1.11e-11!312;UBERON:0000483!1.91e-11!309;UBERON:0002050!8.08e-11!605;UBERON:0005423!8.08e-11!605;UBERON:0000923!1.68e-10!604;UBERON:0005291!1.68e-10!604;UBERON:0006598!1.68e-10!604;UBERON:0002532!1.68e-10!604;UBERON:0000025!4.32e-09!194;UBERON:0004111!7.70e-09!241;UBERON:0000062!7.97e-09!511;UBERON:0003076!1.44e-08!15;UBERON:0003057!1.44e-08!15;UBERON:0000064!1.87e-08!219;UBERON:0000477!2.18e-08!286;UBERON:0004732!2.09e-07!13;UBERON:0002308!4.31e-07!9;UBERON:0000125!4.31e-07!9;UBERON:0002420!4.48e-07!9;UBERON:0007245!4.48e-07!9;UBERON:0010009!4.48e-07!9;UBERON:0010011!4.48e-07!9;UBERON:0000454!4.48e-07!9;UBERON:0004733!9.14e-07!12;UBERON:0002028!9.14e-07!12;UBERON:0007277!9.14e-07!12
}}

Latest revision as of 11:24, 17 September 2013


Full id: C503_occipital_spinal_thalamus_locus_optic_globus_pineal



Phase1 CAGE Peaks

Hg19::chr14:95623976..95624057,+p1@DICER1-AS
Hg19::chr18:46065393..46065444,+p1@CTIF
Hg19::chr1:10436775..10436792,+p@chr1:10436775..10436792
+
Hg19::chr1:66999791..66999798,+p3@SGIP1
Hg19::chr1:67125565..67125577,+p@chr1:67125565..67125577
+
Hg19::chr1:6997068..6997095,+p@chr1:6997068..6997095
+
Hg19::chr3:133380806..133380856,+p1@TFP1
Hg19::chr3:185080917..185080987,+p2@MAP3K13
Hg19::chr4:118006697..118006741,-p1@TRAM1L1
Hg19::chr4:134070293..134070304,-p2@ENST00000509715
Hg19::chr4:71587632..71587646,+p3@RUFY3
Hg19::chr4:71587669..71587752,+p1@RUFY3
Hg19::chr4:71588022..71588055,+p12@RUFY3
Hg19::chr4:85887859..85888004,+p1@WDFY3-AS2
Hg19::chr5:133706714..133706743,-p1@CDKL3
Hg19::chr5:81574463..81574494,+p@chr5:81574463..81574494
+
Hg19::chr7:86781858..86781879,+p3@DMTF1
Hg19::chrX:100740401..100740449,+p1@ARMCX4
Hg19::chrX:102585134..102585176,+p1@TCEAL7


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

No GOStat results

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
nervous system8.31e-4489
central nervous system1.28e-4181
adult organism1.33e-39114
neural tube2.95e-3656
neural rod2.95e-3656
future spinal cord2.95e-3656
neural keel2.95e-3656
neurectoderm5.94e-3586
brain8.57e-3568
future brain8.57e-3568
regional part of nervous system4.56e-3453
regional part of brain4.56e-3453
neural plate2.96e-3382
presumptive neural plate2.96e-3382
ectoderm-derived structure3.78e-31171
ectoderm3.78e-31171
presumptive ectoderm3.78e-31171
regional part of forebrain1.41e-2841
forebrain1.41e-2841
anterior neural tube1.41e-2841
future forebrain1.41e-2841
pre-chordal neural plate7.65e-2561
structure with developmental contribution from neural crest1.93e-24132
brain grey matter9.08e-2434
gray matter9.08e-2434
ecto-epithelium1.09e-23104
telencephalon1.16e-2334
cerebral hemisphere2.16e-2232
regional part of telencephalon2.34e-2232
organ system subdivision9.17e-20223
cerebral cortex1.18e-1725
pallium1.18e-1725
regional part of cerebral cortex7.50e-1722
neocortex2.05e-1520
multi-cellular organism9.72e-14656
anatomical cluster4.21e-12373
multi-tissue structure1.55e-11342
anatomical system6.37e-09624
posterior neural tube8.29e-0915
chordal neural plate8.29e-0915
anatomical group1.23e-08625
organ4.97e-08503
basal ganglion1.38e-079
nuclear complex of neuraxis1.38e-079
aggregate regional part of brain1.38e-079
collection of basal ganglia1.38e-079
cerebral subcortex1.38e-079
neural nucleus1.47e-079
nucleus of brain1.47e-079
embryo1.48e-07592
segmental subdivision of nervous system1.63e-0713
germ layer1.73e-07560
germ layer / neural crest1.73e-07560
embryonic tissue1.73e-07560
presumptive structure1.73e-07560
germ layer / neural crest derived structure1.73e-07560
epiblast (generic)1.73e-07560
embryonic structure2.58e-07564
organ part3.37e-07218
cell layer5.02e-07309
epithelium7.80e-07306
segmental subdivision of hindbrain8.09e-0712
hindbrain8.09e-0712
presumptive hindbrain8.09e-0712
developing anatomical structure9.99e-07581


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)
MA0003.10.325763
MA0004.11.68872
MA0006.10.308609
MA0007.10.180248
MA0009.10.580032
MA0014.10.374383
MA0017.10.114723
MA0019.10.305657
MA0024.12.11236
MA0025.10.70396
MA0027.12.15732
MA0028.10.680413
MA0029.10.50258
MA0030.10.492344
MA0031.10.435419
MA0038.10.743126
MA0040.10.507819
MA0041.10.206566
MA0042.10.183918
MA0043.10.580321
MA0046.10.570066
MA0048.10.716475
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.11.15636
MA0056.10
MA0057.10.976504
MA0058.13.29322
MA0059.10.805771
MA0060.11.404
MA0061.10.121714
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.10.671958
MA0069.10.566544
MA0070.10.556335
MA0071.10.240074
MA0072.10.552241
MA0073.10.934416
MA0074.10.265952
MA0076.10.852336
MA0077.10.545231
MA0078.10.346453
MA0081.10.405301
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.10.398465
MA0089.10
MA0090.10.149167
MA0091.11.07936
MA0092.10.168981
MA0093.12.82138
MA0095.10
MA0098.10
MA0100.10.768006
MA0101.10.0959778
MA0103.10.295078
MA0105.10.035705
MA0106.11.48277
MA0107.10.214555
MA0108.20.432749
MA0109.10
MA0111.10.928951
MA0113.10.315797
MA0114.10.0569149
MA0115.10.805883
MA0116.10.219141
MA0117.10.614633
MA0119.11.2467
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.27535
MA0139.10.0257123
MA0140.10.669735
MA0141.10.128074
MA0142.10.407878
MA0143.10.315941
MA0144.10.0508083
MA0145.10.278749
MA0146.10.306103
MA0147.10.838322
MA0148.10.211171
MA0149.11.21757
MA0062.20.517764
MA0035.20.668495
MA0039.20.515695
MA0138.20.347473
MA0002.21.32966
MA0137.20.342218
MA0104.20.627988
MA0047.20.292798
MA0112.20.0591493
MA0065.20.156004
MA0150.10.446185
MA0151.10
MA0152.10.243034
MA0153.10.67139
MA0154.10.100086
MA0155.10.124291
MA0156.10.703429
MA0157.10.384449
MA0158.10
MA0159.10.487475
MA0160.10.222325
MA0161.10
MA0162.10.00688807
MA0163.10.178355
MA0164.10.870085
MA0080.20.31321
MA0018.20.819991
MA0099.20.243305
MA0079.20.312405
MA0102.21.09681
MA0258.10.177641
MA0259.10.235101
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
POLR2A#5430151.69535777096690.004160730889787010.0198276406916621
SRF#672253.6308363847810.009828519324532970.036941041844564
TRIM28#1015554.892243432963820.002770097925405220.0151763236233224
USF1#7391124.017789017183973.83675826695491e-060.00012537772110216
USF2#739253.418999311860420.01257386612071660.0454709835104403
YY1#7528123.101792052539285.99478432712854e-050.000985967370615712



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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