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{{Coexpression_clusters
{
|full_id=C1808_thalamus_substantia_Eosinophils_globus_CD14_optic_Neutrophils
 

Latest revision as of 11:52, 17 September 2013


Full id: C1808_thalamus_substantia_Eosinophils_globus_CD14_optic_Neutrophils



Phase1 CAGE Peaks

Hg19::chr19:11457233..11457257,+p2@CCDC159
Hg19::chr4:15004067..15004113,+p1@CPEB2
Hg19::chr5:65221552..65221616,+p@chr5:65221552..65221616
+
Hg19::chr6:163835167..163835226,+p7@QKI
Hg19::chr6:163835734..163835758,+p1@QKI


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:0006417regulation of translation0.000758142443290168
GO:0031326regulation of cellular biosynthetic process0.000758142443290168
GO:0009889regulation of biosynthetic process0.000758142443290168
GO:0051246regulation of protein metabolic process0.00215522757872212
GO:0003723RNA binding0.0092540737721995
GO:0006412translation0.0117723159075332
GO:0009059macromolecule biosynthetic process0.016945573322919
GO:0044249cellular biosynthetic process0.0216358830215907
GO:0051028mRNA transport0.0216358830215907
GO:0009058biosynthetic process0.0216358830215907
GO:0050658RNA transport0.0216358830215907
GO:0051236establishment of RNA localization0.0216358830215907
GO:0050657nucleic acid transport0.0216358830215907
GO:0006403RNA localization0.0216358830215907
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0228233871901247
GO:0010468regulation of gene expression0.0416891970694574
GO:0008380RNA splicing0.0416891970694574
GO:0031323regulation of cellular metabolic process0.0416891970694574
GO:0019222regulation of metabolic process0.0439740545531343
GO:0006397mRNA processing0.0448216054292201



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
myeloid leukocyte7.93e-3372
granulocyte monocyte progenitor cell2.33e-2967
macrophage dendritic cell progenitor1.09e-2861
monopoietic cell1.11e-2759
monocyte1.11e-2759
monoblast1.11e-2759
promonocyte1.11e-2759
leukocyte4.46e-27136
myeloid lineage restricted progenitor cell2.18e-2666
defensive cell4.27e-2648
phagocyte4.27e-2648
classical monocyte3.52e-2542
CD14-positive, CD16-negative classical monocyte3.52e-2542
hematopoietic lineage restricted progenitor cell1.43e-20120
nongranular leukocyte1.79e-20115
myeloid cell2.12e-19108
common myeloid progenitor2.12e-19108
hematopoietic stem cell1.34e-18168
angioblastic mesenchymal cell1.34e-18168
hematopoietic oligopotent progenitor cell1.02e-16161
hematopoietic multipotent progenitor cell1.02e-16161
hematopoietic cell6.29e-16177
stuff accumulating cell3.16e-1187
Uber Anatomy
Ontology termp-valuen
adult organism1.70e-29114
hematopoietic system1.87e-2598
blood island1.87e-2598
hemolymphoid system4.04e-25108
bone marrow4.81e-2476
neural tube2.47e-2356
neural rod2.47e-2356
future spinal cord2.47e-2356
neural keel2.47e-2356
immune system4.43e-2393
bone element9.84e-2382
regional part of nervous system1.03e-2153
regional part of brain1.03e-2153
skeletal system5.16e-20100
skeletal element5.58e-2090
central nervous system2.46e-1881
regional part of forebrain9.99e-1841
forebrain9.99e-1841
anterior neural tube9.99e-1841
future forebrain9.99e-1841
brain1.36e-1768
future brain1.36e-1768
brain grey matter3.09e-1734
gray matter3.09e-1734
telencephalon4.42e-1734
regional part of telencephalon4.89e-1632
nervous system7.90e-1689
cerebral hemisphere8.33e-1632
neural plate3.11e-1582
presumptive neural plate3.11e-1582
neurectoderm2.68e-1486
cerebral cortex5.29e-1225
pallium5.29e-1225
regional part of cerebral cortex8.33e-1122
pre-chordal neural plate4.48e-1061
neocortex9.86e-1020
structure with developmental contribution from neural crest4.91e-09132
ecto-epithelium1.59e-08104
posterior neural tube7.76e-0715
chordal neural plate7.76e-0715
neural nucleus7.92e-079
nucleus of brain7.92e-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)
MA0003.13.23705
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.15.83725
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
MA0048.11.7027
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.01397
MA0056.10
MA0057.11.05691
MA0058.11.29981
MA0059.11.29682
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
MA0073.12.92967
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.11.00065
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
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.946108
MA0147.11.00307
MA0148.10.653474
MA0149.11.63245
MA0062.20.284987
MA0035.20.691506
MA0039.23.98195
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.21.96224
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.11.3196
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.14.22787
MA0163.13.78273
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.213.0494
MA0102.21.66336
MA0258.10.914277
MA0259.11.02361
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#90545.068961261570110.002709998091280770.0148970730383321
CTBP2#1488225.08680013573130.002461438599678380.0138500180977216
E2F1#186954.907389214879320.0003512818099256460.00352866412877027
E2F6#187644.013724585357910.006632118233933880.0282980674197745
EGR1#195843.990543275848110.0067800983001440.0287672836225366
ELF1#199754.258097958807540.0007142416939776840.00573143974470498
ETS1#211335.83725655332140.009253279045631430.0349753251871702
HEY1#2346254.040111043105710.0009288852205177990.00674302102909977
MYC#460944.177825497287520.005691969036823440.0256798805234266
NRF1#489937.326167668626540.004839689817117540.0226894269789441
TAF1#687253.343046285745290.002394600090870310.0135373843721124
TBP#690853.706770687096390.001428755106721120.00918885119717023
ZBTB7A#5134157.35190930787594.65425347594289e-050.000815990563662916



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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