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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:23, 17 September 2013


Full id: C466_cerebellum_retinoblastoma_pineal_small_pituitary_parietal_pons



Phase1 CAGE Peaks

Hg19::chr11:17785684..17785695,+p@chr11:17785684..17785695
+
Hg19::chr18:35128158..35128201,-p@chr18:35128158..35128201
-
Hg19::chr18:35145981..35146017,-p3@CELF4
Hg19::chr20:24945160..24945169,-p@chr20:24945160..24945169
-
Hg19::chr7:149700383..149700403,-p@chr7:149700383..149700403
-
Hg19::chr7:149700477..149700562,-p@chr7:149700477..149700562
-
Hg19::chr7:149700569..149700636,-p@chr7:149700569..149700636
-
Hg19::chr7:149700639..149700651,-p@chr7:149700639..149700651
-
Hg19::chr7:149700652..149700676,-p@chr7:149700652..149700676
-
Hg19::chr7:149700678..149700703,-p@chr7:149700678..149700703
-
Hg19::chr7:149700712..149700747,-p@chr7:149700712..149700747
-
Hg19::chr7:149700748..149700770,-p@chr7:149700748..149700770
-
Hg19::chr7:149700790..149700823,-p@chr7:149700790..149700823
-
Hg19::chr7:149700827..149700889,-p@chr7:149700827..149700889
-
Hg19::chr7:149700989..149701027,-p@chr7:149700989..149701027
-
Hg19::chr7:149701365..149701397,-p@chr7:149701365..149701397
-
Hg19::chr7:149701457..149701484,-p@chr7:149701457..149701484
-
Hg19::chr7:149745353..149745375,-p@chr7:149745353..149745375
-
Hg19::chr7:153790013..153790040,+p@chr7:153790013..153790040
+
Hg19::chr7:153790151..153790200,+p@chr7:153790151..153790200
+
Hg19::chr7:153931630..153931643,+p@chr7:153931630..153931643
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube2.25e-6756
neural rod2.25e-6756
future spinal cord2.25e-6756
neural keel2.25e-6756
regional part of nervous system3.26e-6253
regional part of brain3.26e-6253
central nervous system2.21e-5881
nervous system9.50e-5889
brain1.16e-5168
future brain1.16e-5168
regional part of forebrain1.23e-5041
forebrain1.23e-5041
anterior neural tube1.23e-5041
future forebrain1.23e-5041
neurectoderm5.97e-4786
adult organism1.09e-46114
neural plate1.73e-4582
presumptive neural plate1.73e-4582
brain grey matter6.19e-3934
gray matter6.19e-3934
telencephalon1.50e-3834
ecto-epithelium2.73e-37104
regional part of telencephalon1.70e-3532
cerebral hemisphere2.00e-3532
pre-chordal neural plate1.47e-3461
ectoderm-derived structure1.06e-28171
ectoderm1.06e-28171
presumptive ectoderm1.06e-28171
regional part of cerebral cortex1.29e-2822
structure with developmental contribution from neural crest1.69e-27132
organ system subdivision7.96e-26223
neocortex3.18e-2520
cerebral cortex1.40e-2425
pallium1.40e-2425
posterior neural tube4.00e-1715
chordal neural plate4.00e-1715
neural nucleus1.98e-169
nucleus of brain1.98e-169
basal ganglion3.83e-169
nuclear complex of neuraxis3.83e-169
aggregate regional part of brain3.83e-169
collection of basal ganglia3.83e-169
cerebral subcortex3.83e-169
tube1.49e-15192
diencephalon9.30e-147
future diencephalon9.30e-147
anatomical cluster2.46e-13373
telencephalic nucleus6.43e-137
segmental subdivision of hindbrain1.99e-1212
hindbrain1.99e-1212
presumptive hindbrain1.99e-1212
brainstem9.27e-126
segmental subdivision of nervous system2.67e-1113
anatomical conduit9.44e-11240
parietal lobe5.58e-105
limbic system5.90e-105
temporal lobe2.16e-096
gland of diencephalon3.52e-094
neuroendocrine gland3.52e-094
epithelium4.38e-09306
cell layer7.63e-09309
regional part of diencephalon8.18e-094
small intestine1.92e-084
corpus striatum3.40e-084
striatum3.40e-084
ventral part of telencephalon3.40e-084
future corpus striatum3.40e-084
multi-tissue structure3.92e-08342
regional part of metencephalon4.54e-089
metencephalon4.54e-089
future metencephalon4.54e-089
embryo5.91e-08592
gyrus9.45e-086
developing anatomical structure1.28e-07581
germ layer2.21e-07560
germ layer / neural crest2.21e-07560
embryonic tissue2.21e-07560
presumptive structure2.21e-07560
germ layer / neural crest derived structure2.21e-07560
epiblast (generic)2.21e-07560
embryonic structure3.60e-07564
pons4.69e-073
male reproductive organ6.63e-0711


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)
MA0003.10.00063637
MA0004.10.505176
MA0006.13.21264
MA0007.10.924144
MA0009.10.543169
MA0014.10.0596512
MA0017.10.0964051
MA0019.10.275941
MA0024.10.450307
MA0025.10.665335
MA0027.12.11401
MA0028.10.0843345
MA0029.10.467171
MA0030.10.457153
MA0031.10.401568
MA0038.10.24162
MA0040.10.472301
MA0041.10.181587
MA0042.110.4327
MA0043.10.543454
MA0046.10.533373
MA0048.10.00619675
MA0050.10.160894
MA0051.10.238478
MA0052.10.475699
MA0055.10.000311203
MA0056.10
MA0057.10.00555109
MA0058.10.35609
MA0059.11.73026
MA0060.10.0296044
MA0061.10.0219462
MA0063.10
MA0066.10.678752
MA0067.10.83875
MA0068.10.562572
MA0069.10.529912
MA0070.10.519883
MA0071.10.213282
MA0072.10.515863
MA0073.1244.227
MA0074.10.23792
MA0076.10.119431
MA0077.10.508982
MA0078.10.31524
MA0081.10.109654
MA0083.10.549943
MA0084.11.01907
MA0087.10.513678
MA0088.10.0366926
MA0089.10
MA0090.10.402075
MA0091.10.170864
MA0092.10.146372
MA0093.10.268179
MA0095.10
MA0098.10
MA0100.10.252028
MA0101.10.0794742
MA0103.10.251512
MA0105.10.0756894
MA0106.10.272934
MA0107.10.046982
MA0108.20.398967
MA0109.10
MA0111.10.136202
MA0113.10.285689
MA0114.10.17185
MA0115.10.766188
MA0116.10.182019
MA0117.10.577217
MA0119.10.100647
MA0122.10.600851
MA0124.10.727093
MA0125.10.648747
MA0130.10
MA0131.10.329895
MA0132.10
MA0133.10
MA0135.10.570637
MA0136.10.246897
MA0139.10.018888
MA0140.10.211376
MA0141.10.108582
MA0142.10.374765
MA0143.10.285827
MA0144.10.0397909
MA0145.10.00212809
MA0146.11.04313e-05
MA0147.10.186237
MA0148.10.185927
MA0149.10.204488
MA0062.20.0205944
MA0035.20.210872
MA0039.27.90025e-05
MA0138.20.316226
MA0002.25.03825
MA0137.20.0876366
MA0104.20.0293723
MA0047.20.263601
MA0112.20.0117779
MA0065.20.00228314
MA0150.10.393024
MA0151.10
MA0152.10.216094
MA0153.10.633172
MA0154.10.00405158
MA0155.10.303035
MA0156.10.0888107
MA0157.10.352016
MA0158.10
MA0159.10.734091
MA0160.10.196462
MA0161.10
MA0162.10.595981
MA0163.10.066224
MA0164.10.295453
MA0080.20.0778984
MA0018.20.274004
MA0099.20.618776
MA0079.29.9942e-06
MA0102.21.05522
MA0258.10.336256
MA0259.10.196503
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
MYC#4609102.486800891242570.002914290739054180.0157473929271564
NR2C2#71821015.53076709773371.88496708895321e-101.96079758768112e-08



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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