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{{Coexpression_clusters
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of transcription, DNA-dependent!0.0424766712495599!284443;353088$GO:0006351!transcription, DNA-dependent!0.0424766712495599!284443;353088$GO:0032774!RNA biosynthetic process!0.0424766712495599!284443;353088$GO:0003677!DNA binding!0.0424766712495599!284443;353088$GO:0045449!regulation of transcription!0.0424766712495599!284443;353088$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0424766712495599!284443;353088$GO:0006350!transcription!0.0424766712495599!284443;353088$GO:0010468!regulation of gene expression!0.0424766712495599!284443;353088$GO:0031323!regulation of cellular metabolic process!0.0424766712495599!284443;353088$GO:0019222!regulation of metabolic process!0.0424766712495599!284443;353088$GO:0016070!RNA metabolic process!0.0424766712495599!284443;353088$GO:0008270!zinc ion 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|full_id=C3688_Eosinophils_cerebellum_thymus_Neutrophils_optic_CD4_occipital
|gostat_on_coexpression_clusters=GO:0006355!regulation of transcription, DNA-dependent!0.0424766712495599!284443;353088$GO:0006351!transcription, DNA-dependent!0.0424766712495599!284443;353088$GO:0032774!RNA biosynthetic process!0.0424766712495599!284443;353088$GO:0003677!DNA binding!0.0424766712495599!284443;353088$GO:0045449!regulation of transcription!0.0424766712495599!284443;353088$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0424766712495599!284443;353088$GO:0006350!transcription!0.0424766712495599!284443;353088$GO:0010468!regulation of gene expression!0.0424766712495599!284443;353088$GO:0031323!regulation of cellular metabolic process!0.0424766712495599!284443;353088$GO:0019222!regulation of metabolic process!0.0424766712495599!284443;353088$GO:0016070!RNA metabolic process!0.0424766712495599!284443;353088$GO:0008270!zinc ion binding!0.0424766712495599!284443;353088
|id=C3688
}}

Latest revision as of 12:31, 17 September 2013


Full id: C3688_Eosinophils_cerebellum_thymus_Neutrophils_optic_CD4_occipital



Phase1 CAGE Peaks

Hg19::chr17:75954770..75954796,+p@chr17:75954770..75954796
+
Hg19::chr19:21579908..21579949,+p1@ZNF493
Hg19::chr19:21688387..21688432,+p1@ZNF429


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-dependent0.0424766712495599
GO:0006351transcription, DNA-dependent0.0424766712495599
GO:0032774RNA biosynthetic process0.0424766712495599
GO:0003677DNA binding0.0424766712495599
GO:0045449regulation of transcription0.0424766712495599
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0424766712495599
GO:0006350transcription0.0424766712495599
GO:0010468regulation of gene expression0.0424766712495599
GO:0031323regulation of cellular metabolic process0.0424766712495599
GO:0019222regulation of metabolic process0.0424766712495599
GO:0016070RNA metabolic process0.0424766712495599
GO:0008270zinc ion binding0.0424766712495599



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 organism1.59e-44114
neural tube6.17e-2856
neural rod6.17e-2856
future spinal cord6.17e-2856
neural keel6.17e-2856
central nervous system2.19e-2781
nervous system8.14e-2789
regional part of nervous system3.13e-2653
regional part of brain3.13e-2653
brain4.97e-2368
future brain4.97e-2368
regional part of forebrain1.43e-2241
forebrain1.43e-2241
anterior neural tube1.43e-2241
future forebrain1.43e-2241
neurectoderm5.54e-2086
neural plate9.52e-2082
presumptive neural plate9.52e-2082
brain grey matter1.46e-1834
gray matter1.46e-1834
telencephalon2.02e-1834
regional part of telencephalon2.08e-1732
cerebral hemisphere2.63e-1732
pre-chordal neural plate2.53e-1561
regional part of cerebral cortex9.72e-1422
cerebral cortex2.35e-1325
pallium2.35e-1325
neocortex1.11e-1220
ecto-epithelium1.68e-12104
ectoderm-derived structure4.26e-12171
ectoderm4.26e-12171
presumptive ectoderm4.26e-12171
organ system subdivision8.69e-09223
structure with developmental contribution from neural crest1.52e-08132
basal ganglion8.99e-079
nuclear complex of neuraxis8.99e-079
aggregate regional part of brain8.99e-079
collection of basal ganglia8.99e-079
cerebral subcortex8.99e-079
neural nucleus9.97e-079
nucleus of brain9.97e-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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.10.714521
MA0060.12.13518
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
ELF1#199734.258097958807540.01295179875054610.0461836494830238
GABPB1#255337.067683836182170.002832212825417420.0153986920336181
IRF1#365937.63716375356390.002244692747297240.0127965865630446
NFYA#4800318.42558069983050.0001598135507814160.00199483296642289
NFYB#4801316.75979325353650.0002123649923296180.00245671105825354
PBX3#5090214.60967512449610.006056122473217890.0268267962412692
RFX5#5993312.04791082719510.0005717246050312580.00484308103048581
SP1#666735.69838137814090.005403962701712170.0246273273379638
SP2#6668217.43568699589640.004273568481769740.0203162282610747
TAF7#6879311.43306940492390.0006690181981945830.00542354976335047
YY1#752834.911170749853860.008441455341808260.0329035289409238



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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