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Coexpression cluster:C3085: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3085_Eosinophils_Neutrophils_optic_granulocyte_CD14_CD8_globus
|id=C3085
}}

Latest revision as of 12:18, 17 September 2013


Full id: C3085_Eosinophils_Neutrophils_optic_granulocyte_CD14_CD8_globus



Phase1 CAGE Peaks

Hg19::chr11:116969131..116969166,-p1@SIK3
Hg19::chrX:153363125..153363182,-p1@MECP2
Hg19::chrX:44732455..44732473,+p2@KDM6A


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
leukocyte1.91e-30136
hematopoietic stem cell1.48e-26168
angioblastic mesenchymal cell1.48e-26168
hematopoietic lineage restricted progenitor cell1.43e-25120
hematopoietic oligopotent progenitor cell7.29e-25161
hematopoietic multipotent progenitor cell7.29e-25161
hematopoietic cell7.09e-24177
nongranular leukocyte4.49e-23115
classical monocyte3.20e-2242
CD14-positive, CD16-negative classical monocyte3.20e-2242
myeloid leukocyte3.84e-2072
granulocyte monocyte progenitor cell9.79e-1867
defensive cell2.84e-1748
phagocyte2.84e-1748
myeloid cell7.57e-17108
common myeloid progenitor7.57e-17108
myeloid lineage restricted progenitor cell1.14e-1666
macrophage dendritic cell progenitor1.13e-1561
monopoietic cell1.12e-1459
monocyte1.12e-1459
monoblast1.12e-1459
promonocyte1.12e-1459
lymphoid lineage restricted progenitor cell1.84e-0852
nucleate cell2.82e-0855
lymphocyte7.92e-0853
common lymphoid progenitor7.92e-0853
mature alpha-beta T cell1.23e-0718
alpha-beta T cell1.23e-0718
immature T cell1.23e-0718
mature T cell1.23e-0718
immature alpha-beta T cell1.23e-0718
Uber Anatomy
Ontology termp-valuen
adult organism1.46e-35114
hematopoietic system2.13e-2198
blood island2.13e-2198
hemolymphoid system2.84e-18108
neural tube3.42e-1856
neural rod3.42e-1856
future spinal cord3.42e-1856
neural keel3.42e-1856
regional part of nervous system8.50e-1753
regional part of brain8.50e-1753
bone element2.24e-1582
bone marrow4.20e-1576
regional part of forebrain1.48e-1441
forebrain1.48e-1441
anterior neural tube1.48e-1441
future forebrain1.48e-1441
immune system9.34e-1493
central nervous system6.93e-1381
brain5.99e-1268
future brain5.99e-1268
nervous system8.50e-1289
brain grey matter1.24e-1134
gray matter1.24e-1134
telencephalon1.50e-1134
neural plate3.48e-1182
presumptive neural plate3.48e-1182
neurectoderm5.17e-1186
skeletal element8.56e-1190
regional part of telencephalon1.02e-1032
cerebral hemisphere1.92e-1032
regional part of cerebral cortex2.75e-0922
skeletal system3.65e-09100
neocortex1.88e-0820
pre-chordal neural plate4.94e-0861
cerebral cortex9.42e-0825
pallium9.42e-0825


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)
MA0003.11.54338
MA0004.11.93041
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.12.4146
MA0058.11.70328
MA0059.10.714521
MA0060.13.15662
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
MA0073.10.211629
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
MA0093.11.55117
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.22.13692
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
MA0160.12.02335
MA0161.10
MA0162.12.76014
MA0163.14.77883
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.28.812
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
ATF3#467214.97544968400580.005768294540793880.0259446560527981
CCNT2#90536.336201576962630.003930750035764890.0189146518146539
E2F1#186934.907389214879320.008460985347239390.0323589002739247
NFE2#4778251.4695071010860.0004987653528392110.0044054934611954
NFYA#4800212.28372046655370.008516011403724430.0324623591135694
NFYB#4801211.17319550235760.01025467135054530.0381120821742855
PBX3#5090214.60967512449610.006056122473217890.0268086031865555
SP2#6668217.43568699589640.004273568481769740.0203079087572823
SREBF1#6720231.33723296032550.00133816265136180.0088722936227511
YY1#752834.911170749853860.008441455341808260.0327933772668916



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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