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{{Coexpression_clusters
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|full_id=C1940_migratory_thalamus_cord_globus_substantia_hippocampus_CD14CD16
|id=C1940
}}

Latest revision as of 11:55, 17 September 2013


Full id: C1940_migratory_thalamus_cord_globus_substantia_hippocampus_CD14CD16



Phase1 CAGE Peaks

Hg19::chr4:36245643..36245697,-p5@ARAP2
Hg19::chr4:36245700..36245716,-p13@ARAP2
Hg19::chr4:36246367..36246380,-p12@ARAP2
Hg19::chr4:36246391..36246453,-p2@ARAP2
Hg19::chr4:36246458..36246477,-p8@ARAP2


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
leukocyte1.57e-46136
hematopoietic lineage restricted progenitor cell3.11e-40120
nongranular leukocyte7.74e-40115
hematopoietic stem cell1.04e-33168
angioblastic mesenchymal cell1.04e-33168
hematopoietic cell3.12e-33177
hematopoietic oligopotent progenitor cell9.50e-31161
hematopoietic multipotent progenitor cell9.50e-31161
granulocyte monocyte progenitor cell7.77e-2767
macrophage dendritic cell progenitor5.30e-2661
classical monocyte1.90e-2542
CD14-positive, CD16-negative classical monocyte1.90e-2542
myeloid leukocyte4.30e-2572
myeloid lineage restricted progenitor cell7.01e-2566
defensive cell7.22e-2548
phagocyte7.22e-2548
monopoietic cell9.11e-2559
monocyte9.11e-2559
monoblast9.11e-2559
promonocyte9.11e-2559
myeloid cell4.81e-17108
common myeloid progenitor4.81e-17108
lymphoid lineage restricted progenitor cell9.85e-1452
lymphocyte3.31e-1353
common lymphoid progenitor3.31e-1353
nucleate cell3.21e-1255
T cell5.39e-1025
pro-T cell5.39e-1025
mature alpha-beta T cell5.61e-1018
alpha-beta T cell5.61e-1018
immature T cell5.61e-1018
mature T cell5.61e-1018
immature alpha-beta T cell5.61e-1018
dendritic cell5.71e-0910
conventional dendritic cell1.20e-078
intermediate monocyte1.96e-079
CD14-positive, CD16-positive monocyte1.96e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.37e-3298
blood island5.37e-3298
adult organism1.09e-31114
neural tube4.06e-2856
neural rod4.06e-2856
future spinal cord4.06e-2856
neural keel4.06e-2856
hemolymphoid system6.87e-28108
regional part of nervous system7.41e-2653
regional part of brain7.41e-2653
regional part of forebrain2.12e-2241
forebrain2.12e-2241
anterior neural tube2.12e-2241
future forebrain2.12e-2241
bone marrow7.11e-2276
immune system1.14e-2193
bone element6.13e-2082
telencephalon1.73e-1834
brain grey matter2.41e-1834
gray matter2.41e-1834
central nervous system6.04e-1881
brain1.69e-1768
future brain1.69e-1768
regional part of telencephalon5.94e-1732
skeletal element7.87e-1790
cerebral hemisphere7.92e-1732
neural plate1.26e-1582
presumptive neural plate1.26e-1582
nervous system5.01e-1589
skeletal system1.50e-14100
neurectoderm5.27e-1486
pre-chordal neural plate2.43e-1261
regional part of cerebral cortex9.74e-1222
cerebral cortex2.65e-1125
pallium2.65e-1125
neocortex2.90e-1020
ecto-epithelium1.62e-09104
neural nucleus3.91e-099
nucleus of brain3.91e-099
telencephalic nucleus9.49e-087
blood2.14e-0715
haemolymphatic fluid2.14e-0715
organism substance2.14e-0715
basal ganglion2.28e-079
nuclear complex of neuraxis2.28e-079
aggregate regional part of brain2.28e-079
collection of basal ganglia2.28e-079
cerebral subcortex2.28e-079
posterior neural tube5.59e-0715
chordal neural plate5.59e-0715


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)
MA0003.11.40197
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.11.44118
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.11.73427
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.13.01022
MA0103.11.12656
MA0105.11.00065
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.442008
MA0146.11.35428
MA0147.11.77656
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.13.53221
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0198381
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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#186954.907389214879320.0003512818099256460.00353444325113916
EBF1#187935.34388010794140.01187615563868110.0432458358756048
GATA3#2625210.89460654288240.0125158291218830.0452861931007602
MAFK#7975316.26043988269790.0004748211423830540.00435801435006097
TAF1#687253.343046285745290.002394600090870310.0135527902720644



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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