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{{Coexpression_clusters
{
|full_id=C1402_hippocampus_occipital_medial_pineal_temporal_parietal_amygdala
|

Latest revision as of 11:44, 17 September 2013


Full id: C1402_hippocampus_occipital_medial_pineal_temporal_parietal_amygdala



Phase1 CAGE Peaks

Hg19::chr14:93651186..93651265,-p1@MOAP1
Hg19::chr18:32621351..32621421,+p1@MAPRE2
Hg19::chr18:54318893..54318941,+p@chr18:54318893..54318941
+
Hg19::chr2:99061298..99061377,+p1@INPP4A
Hg19::chr3:14989138..14989151,+p6@NR2C2
Hg19::chr5:156693092..156693150,+p1@CYFIP2


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:0016316phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity0.0367928413934545



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
leukocyte3.53e-34136
hematopoietic stem cell3.79e-31168
angioblastic mesenchymal cell3.79e-31168
nongranular leukocyte6.12e-29115
hematopoietic cell2.97e-28177
hematopoietic oligopotent progenitor cell3.99e-28161
hematopoietic multipotent progenitor cell3.99e-28161
hematopoietic lineage restricted progenitor cell3.80e-27120
myeloid leukocyte3.55e-1672
lymphoid lineage restricted progenitor cell1.22e-1552
lymphocyte1.26e-1553
common lymphoid progenitor1.26e-1553
defensive cell9.62e-1548
phagocyte9.62e-1548
nucleate cell2.50e-1455
classical monocyte9.21e-1442
CD14-positive, CD16-negative classical monocyte9.21e-1442
granulocyte monocyte progenitor cell2.31e-1367
myeloid cell4.15e-13108
common myeloid progenitor4.15e-13108
macrophage dendritic cell progenitor2.59e-1261
monopoietic cell3.76e-1259
monocyte3.76e-1259
monoblast3.76e-1259
promonocyte3.76e-1259
myeloid lineage restricted progenitor cell7.66e-1266
T cell3.05e-1125
pro-T cell3.05e-1125
mature alpha-beta T cell2.18e-1018
alpha-beta T cell2.18e-1018
immature T cell2.18e-1018
mature T cell2.18e-1018
immature alpha-beta T cell2.18e-1018
CD8-positive, alpha-beta T cell6.45e-0711
Uber Anatomy
Ontology termp-valuen
adult organism2.78e-34114
neural tube3.07e-2656
neural rod3.07e-2656
future spinal cord3.07e-2656
neural keel3.07e-2656
regional part of nervous system6.81e-2553
regional part of brain6.81e-2553
central nervous system8.07e-2581
nervous system2.84e-2489
regional part of forebrain3.20e-2241
forebrain3.20e-2241
anterior neural tube3.20e-2241
future forebrain3.20e-2241
brain2.70e-2168
future brain2.70e-2168
brain grey matter3.32e-1934
gray matter3.32e-1934
telencephalon4.36e-1934
cerebral hemisphere1.37e-1832
regional part of telencephalon4.12e-1832
hematopoietic system2.45e-1698
blood island2.45e-1698
neurectoderm3.77e-1686
neural plate4.45e-1682
presumptive neural plate4.45e-1682
regional part of cerebral cortex1.27e-1522
cerebral cortex9.41e-1525
pallium9.41e-1525
hemolymphoid system1.43e-14108
neocortex2.00e-1420
pre-chordal neural plate1.81e-1261
immune system1.22e-1093
bone marrow3.91e-1076
bone element1.32e-0982
ecto-epithelium5.64e-09104


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)
MA0003.15.21839
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.13.70108
MA0017.12.88372
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.147053
MA0058.11.16137
MA0059.11.15845
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0569999
MA0074.10.660398
MA0076.11.19721
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.11.52717
MA0115.12.85672
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.19942
MA0140.10.622527
MA0141.11.15452
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.13.00011
MA0146.12.38407
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.21.22729
MA0035.20.621793
MA0039.23.23723
MA0138.20.765223
MA0002.21.3092
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.680553
MA0065.21.18263
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.14.31015
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.12.40092
MA0163.11.60684
MA0164.10.738243
MA0080.20.394469
MA0018.21.69036
MA0099.20.629739
MA0079.22.88163
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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#90544.224134384641760.007109805478875810.0296104388247522
E2F4#187436.334030157642220.008197175368374340.0323595705434551
ELF1#199753.548414965672950.003446837775721690.0175302795450985
HEY1#2346264.040111043105710.0002298968555807510.00253138615708993
NFKB1#479054.57338618682820.00102196259371130.00724446829054599
NR2C2#7182210.87153696841360.01298583020012040.0460815847327777
POLR2A#543062.147453176558070.01019570676818780.0380160449540438
TAF1#687263.343046285745290.0007162474284635620.00572992456386871



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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