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{{Coexpression_clusters
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|full_id=C4796_salivary_CD14_submaxillary_left_Monocytederived_Whole_Macrophage
|id=C4796
}}

Latest revision as of 14:19, 17 September 2013


Full id: C4796_salivary_CD14_submaxillary_left_Monocytederived_Whole_Macrophage



Phase1 CAGE Peaks

Hg19::chr9:124262091..124262114,-p1@GGTA1P
Hg19::chr9:124262117..124262140,-p2@GGTA1P
Hg19::chr9:124262141..124262167,-p4@GGTA1P


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
granulocyte monocyte progenitor cell2.96e-3467
macrophage dendritic cell progenitor2.73e-3361
myeloid leukocyte2.75e-3372
monopoietic cell1.68e-3159
monocyte1.68e-3159
monoblast1.68e-3159
promonocyte1.68e-3159
myeloid lineage restricted progenitor cell2.30e-3166
defensive cell9.69e-3148
phagocyte9.69e-3148
myeloid cell1.18e-26108
common myeloid progenitor1.18e-26108
classical monocyte1.12e-2542
CD14-positive, CD16-negative classical monocyte1.12e-2542
leukocyte8.67e-19136
hematopoietic stem cell4.58e-16168
angioblastic mesenchymal cell4.58e-16168
hematopoietic lineage restricted progenitor cell5.36e-15120
hematopoietic oligopotent progenitor cell1.99e-14161
hematopoietic multipotent progenitor cell1.99e-14161
hematopoietic cell3.40e-14177
nongranular leukocyte7.74e-14115
stuff accumulating cell2.04e-1287
dendritic cell1.47e-0710
conventional dendritic cell3.33e-078
Uber Anatomy
Ontology termp-valuen
adult organism7.76e-62114
hemolymphoid system1.18e-35108
hematopoietic system2.95e-3598
blood island2.95e-3598
immune system6.49e-2993
bone marrow1.72e-2876
bone element2.11e-2582
skeletal element5.35e-2190
lateral plate mesoderm4.49e-20203
neural tube3.18e-1856
neural rod3.18e-1856
future spinal cord3.18e-1856
neural keel3.18e-1856
skeletal system4.48e-18100
regional part of nervous system1.60e-1653
regional part of brain1.60e-1653
regional part of forebrain9.60e-1641
forebrain9.60e-1641
anterior neural tube9.60e-1641
future forebrain9.60e-1641
telencephalon4.86e-1334
brain grey matter9.20e-1334
gray matter9.20e-1334
regional part of telencephalon4.64e-1232
cerebral hemisphere5.57e-1232
neural plate3.02e-1182
presumptive neural plate3.02e-1182
brain6.30e-1168
future brain6.30e-1168
regional part of cerebral cortex1.01e-1022
central nervous system1.41e-1081
germ layer5.35e-10560
germ layer / neural crest5.35e-10560
embryonic tissue5.35e-10560
presumptive structure5.35e-10560
germ layer / neural crest derived structure5.35e-10560
epiblast (generic)5.35e-10560
neurectoderm5.36e-1086
embryonic structure5.95e-10564
neocortex1.99e-0920
organ4.19e-09503
developing anatomical structure6.20e-09581
mesoderm1.07e-08315
mesoderm-derived structure1.07e-08315
presumptive mesoderm1.07e-08315
cerebral cortex1.17e-0825
pallium1.17e-0825
anatomical system1.50e-08624
embryo1.67e-08592
anatomical group1.93e-08625
multi-cellular organism2.60e-08656
nervous system4.42e-0889
tissue1.23e-07773
pre-chordal neural plate1.53e-0761
blood1.67e-0715
haemolymphatic fluid1.67e-0715
organism substance1.67e-0715
structure with developmental contribution from neural crest1.77e-07132
ecto-epithelium5.09e-07104


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)
MA0003.12.05336
MA0004.11.93041
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0059.11.70014
MA0060.10.492218
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
MA0073.14.54482
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
MA0093.12.626
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
MA0119.12.7939
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
MA0145.10.273764
MA0146.11.16674
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
E2F1#186934.907389214879320.008460985347239390.0328131024389281
E2F6#187635.017155731697390.00791769806886330.032472667135834
EGR1#195834.988179094810140.008056488137383440.0322825185919348
MYC#460935.22228187160940.007020843755740150.0296394317072536
SUZ12#23512350.11578091106297.93834897779404e-060.000223771451792667
USF1#739136.361499277207960.00388404057290560.0191342128959287
ZNF263#1012738.221841637010680.001799043925565870.0110225477262803



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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