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Coexpression cluster:C4299: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4299_Dendritic_parietal_temporal_occipital_pituitary_gastrointestinal_cerebellum
|id=C4299
}}

Latest revision as of 12:43, 17 September 2013


Full id: C4299_Dendritic_parietal_temporal_occipital_pituitary_gastrointestinal_cerebellum



Phase1 CAGE Peaks

Hg19::chr3:160473343..160473400,+p1@PPM1L
Hg19::chr3:160473403..160473426,+p2@PPM1L
Hg19::chr3:160473436..160473450,+p3@PPM1L


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
macrophage dendritic cell progenitor1.48e-1561
monopoietic cell3.23e-1559
monocyte3.23e-1559
monoblast3.23e-1559
promonocyte3.23e-1559
granulocyte monocyte progenitor cell1.49e-1467
nongranular leukocyte4.41e-14115
myeloid lineage restricted progenitor cell5.63e-1466
leukocyte2.71e-13136
myeloid leukocyte4.62e-1372
hematopoietic lineage restricted progenitor cell6.95e-13120
defensive cell2.79e-1248
phagocyte2.79e-1248
hematopoietic cell6.93e-12177
classical monocyte7.34e-1242
CD14-positive, CD16-negative classical monocyte7.34e-1242
hematopoietic stem cell8.74e-12168
angioblastic mesenchymal cell8.74e-12168
hematopoietic oligopotent progenitor cell6.97e-11161
hematopoietic multipotent progenitor cell6.97e-11161
myeloid cell2.65e-10108
common myeloid progenitor2.65e-10108
stuff accumulating cell1.92e-0787
Uber Anatomy
Ontology termp-valuen
adult organism1.33e-41114
neural tube8.27e-2356
neural rod8.27e-2356
future spinal cord8.27e-2356
neural keel8.27e-2356
regional part of nervous system1.36e-2153
regional part of brain1.36e-2153
central nervous system2.31e-2181
nervous system1.12e-2089
regional part of forebrain6.30e-1941
forebrain6.30e-1941
anterior neural tube6.30e-1941
future forebrain6.30e-1941
neurectoderm4.22e-1886
neural plate8.30e-1882
presumptive neural plate8.30e-1882
brain3.26e-1768
future brain3.26e-1768
telencephalon5.17e-1634
brain grey matter1.02e-1534
gray matter1.02e-1534
cerebral hemisphere1.70e-1532
regional part of telencephalon5.40e-1532
hematopoietic system9.86e-1598
blood island9.86e-1598
pre-chordal neural plate4.10e-1461
regional part of cerebral cortex9.31e-1422
neocortex5.47e-1320
cerebral cortex1.10e-1225
pallium1.10e-1225
hemolymphoid system1.20e-11108
bone marrow1.82e-1176
organ system subdivision2.02e-11223
bone element2.74e-1182
ecto-epithelium5.09e-11104
skeletal element7.43e-1190
ectoderm-derived structure2.69e-10171
ectoderm2.69e-10171
presumptive ectoderm2.69e-10171
immune system2.68e-0993
skeletal system5.54e-09100
structure with developmental contribution from neural crest2.75e-07132


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
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.13.14798
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
MA0058.10.716037
MA0059.10.714521
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
MA0073.10.0185922
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
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
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
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
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
CCNT2#90536.336201576962630.003930750035764890.0190595479356168
E2F1#186934.907389214879320.008460985347239390.032659084476488
E2F6#187635.017155731697390.00791769806886330.0323393221984362
EP300#203336.77394172622320.003216880500103790.016794190579872
IRF1#365937.63716375356390.002244692747297240.0128449655270931
SMARCC2#6601394.15537442689761.19621075407887e-064.86302276937497e-05
STAT1#6772320.70658749719920.0001125992441046670.00155141852968962
USF1#739136.361499277207960.00388404057290560.0190847007007146



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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