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Coexpression cluster:C3247: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3247_Eosinophils_CD14_cerebellum_Neutrophils_brain_occipital_temporal
|id=C3247
}}

Latest revision as of 12:22, 17 September 2013


Full id: C3247_Eosinophils_CD14_cerebellum_Neutrophils_brain_occipital_temporal



Phase1 CAGE Peaks

Hg19::chr12:121734496..121734564,-p1@CAMKK2
Hg19::chr16:11762271..11762344,+p1@SNN
Hg19::chr2:16847115..16847139,-p2@FAM49A


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
myeloid leukocyte1.86e-2872
defensive cell1.05e-2548
phagocyte1.05e-2548
granulocyte monocyte progenitor cell8.26e-2467
classical monocyte1.36e-2342
CD14-positive, CD16-negative classical monocyte1.36e-2342
monopoietic cell4.66e-2359
monocyte4.66e-2359
monoblast4.66e-2359
promonocyte4.66e-2359
macrophage dendritic cell progenitor1.14e-2261
myeloid lineage restricted progenitor cell1.75e-2166
leukocyte2.31e-20136
myeloid cell4.76e-18108
common myeloid progenitor4.76e-18108
nongranular leukocyte5.99e-15115
hematopoietic stem cell2.41e-14168
angioblastic mesenchymal cell2.41e-14168
stuff accumulating cell2.54e-1487
hematopoietic cell7.22e-14177
hematopoietic oligopotent progenitor cell1.54e-13161
hematopoietic multipotent progenitor cell1.54e-13161
hematopoietic lineage restricted progenitor cell2.00e-13120
endothelial cell1.97e-0936
endothelial cell of vascular tree2.17e-0724
meso-epithelial cell6.43e-0745
Uber Anatomy
Ontology termp-valuen
adult organism7.75e-29114
hemolymphoid system9.28e-27108
hematopoietic system1.08e-2498
blood island1.08e-2498
neural tube1.59e-2356
neural rod1.59e-2356
future spinal cord1.59e-2356
neural keel1.59e-2356
immune system1.26e-2293
regional part of nervous system1.70e-2253
regional part of brain1.70e-2253
central nervous system2.73e-2281
bone marrow8.59e-2176
nervous system8.35e-2089
neural plate1.39e-1982
presumptive neural plate1.39e-1982
neurectoderm1.58e-1986
brain1.33e-1868
future brain1.33e-1868
bone element2.13e-1882
regional part of forebrain2.67e-1841
forebrain2.67e-1841
anterior neural tube2.67e-1841
future forebrain2.67e-1841
telencephalon3.10e-1734
skeletal element3.47e-1790
brain grey matter5.23e-1734
gray matter5.23e-1734
cerebral hemisphere1.11e-1632
regional part of telencephalon3.21e-1632
skeletal system9.21e-16100
pre-chordal neural plate4.34e-1561
regional part of cerebral cortex3.34e-1422
cerebral cortex4.01e-1325
pallium4.01e-1325
neocortex4.18e-1320
ecto-epithelium2.39e-12104
lateral plate mesoderm3.50e-11203
ectoderm-derived structure5.32e-11171
ectoderm5.32e-11171
presumptive ectoderm5.32e-11171
structure with developmental contribution from neural crest9.30e-11132
tissue4.83e-10773
germ layer9.15e-10560
germ layer / neural crest9.15e-10560
embryonic tissue9.15e-10560
presumptive structure9.15e-10560
germ layer / neural crest derived structure9.15e-10560
epiblast (generic)9.15e-10560
embryonic structure9.55e-10564
developing anatomical structure1.07e-09581
embryo1.70e-09592


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)
MA0003.16.06693
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.18.34001
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.14.54482
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
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
MA0145.12.11725
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.28.82315
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.211.5899
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

No analysis results for this cluster

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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