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Coexpression cluster:C521: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:24, 17 September 2013


Full id: C521_parietal_occipital_middle_amygdala_temporal_medial_hippocampus



Phase1 CAGE Peaks

Hg19::chr10:117443073..117443076,+p@chr10:117443073..117443076
+
Hg19::chr10:117703137..117703140,+p@chr10:117703137..117703140
+
Hg19::chr10:14017810..14017839,-p@chr10:14017810..14017839
-
Hg19::chr10:14017899..14017911,-p@chr10:14017899..14017911
-
Hg19::chr10:83671380..83671394,+p@chr10:83671380..83671394
+
Hg19::chr10:84202570..84202575,+p@chr10:84202570..84202575
+
Hg19::chr10:84220744..84220762,+p@chr10:84220744..84220762
+
Hg19::chr10:84747563..84747567,+p@chr10:84747563..84747567
+
Hg19::chr10:87388190..87388201,-p@chr10:87388190..87388201
-
Hg19::chr11:84145959..84145962,-p@chr11:84145959..84145962
-
Hg19::chr11:88554509..88554513,-p@chr11:88554509..88554513
-
Hg19::chr11:88711638..88711642,-p@chr11:88711638..88711642
-
Hg19::chr12:126140345..126140356,+p5@TMEM132B
Hg19::chr22:50779073..50779082,-p@chr22:50779073..50779082
-
Hg19::chr2:80256787..80256791,+p@chr2:80256787..80256791
+
Hg19::chr4:62163400..62163404,+p@chr4:62163400..62163404
+
Hg19::chr8:133489594..133489598,-p@chr8:133489594..133489598
-


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 tube3.97e-11356
neural rod3.97e-11356
future spinal cord3.97e-11356
neural keel3.97e-11356
regional part of nervous system5.85e-10553
regional part of brain5.85e-10553
central nervous system1.68e-9781
nervous system2.14e-9689
regional part of forebrain4.04e-9341
forebrain4.04e-9341
anterior neural tube4.04e-9341
future forebrain4.04e-9341
brain2.62e-8968
future brain2.62e-8968
neural plate1.09e-7682
presumptive neural plate1.09e-7682
neurectoderm1.20e-7586
brain grey matter4.44e-7534
gray matter4.44e-7534
telencephalon1.04e-7434
regional part of telencephalon1.23e-6932
cerebral hemisphere1.30e-6932
pre-chordal neural plate9.71e-6361
ecto-epithelium1.99e-60104
regional part of cerebral cortex1.12e-5822
neocortex6.40e-5320
adult organism1.69e-51114
cerebral cortex3.78e-5125
pallium3.78e-5125
ectoderm-derived structure1.14e-49171
ectoderm1.14e-49171
presumptive ectoderm1.14e-49171
structure with developmental contribution from neural crest4.12e-47132
organ system subdivision2.02e-36223
tube7.49e-27192
basal ganglion1.58e-259
nuclear complex of neuraxis1.58e-259
aggregate regional part of brain1.58e-259
collection of basal ganglia1.58e-259
cerebral subcortex1.58e-259
neural nucleus3.61e-259
nucleus of brain3.61e-259
posterior neural tube9.39e-2115
chordal neural plate9.39e-2115
telencephalic nucleus6.97e-207
diencephalon2.86e-197
future diencephalon2.86e-197
anatomical conduit6.31e-19240
anatomical cluster1.38e-18373
gyrus1.20e-176
brainstem7.21e-176
limbic system1.20e-155
temporal lobe2.41e-156
occipital lobe4.47e-155
parietal lobe4.61e-155
epithelium1.85e-14306
cell layer3.42e-14309
segmental subdivision of hindbrain6.94e-1412
hindbrain6.94e-1412
presumptive hindbrain6.94e-1412
segmental subdivision of nervous system1.05e-1213
corpus striatum2.51e-124
striatum2.51e-124
ventral part of telencephalon2.51e-124
future corpus striatum2.51e-124
regional part of diencephalon4.99e-124
gland of diencephalon1.38e-114
neuroendocrine gland1.38e-114
organ part4.89e-11218
multi-tissue structure8.18e-11342
frontal cortex4.85e-103
caudate-putamen1.07e-093
dorsal striatum1.07e-093
pons1.80e-093
spinal cord2.26e-093
dorsal region element2.26e-093
dorsum2.26e-093
medulla oblongata4.22e-093
myelencephalon4.22e-093
future myelencephalon4.22e-093
germ layer1.53e-08560
germ layer / neural crest1.53e-08560
embryonic tissue1.53e-08560
presumptive structure1.53e-08560
germ layer / neural crest derived structure1.53e-08560
epiblast (generic)1.53e-08560
embryo2.14e-08592
embryonic structure2.26e-08564
developing anatomical structure3.05e-08581
regional part of metencephalon1.06e-079
metencephalon1.06e-079
future metencephalon1.06e-079
organ1.32e-07503
amygdala2.39e-072
Ammon's horn2.39e-072
lobe parts of cerebral cortex2.39e-072
hippocampal formation2.39e-072
limbic lobe2.39e-072
middle frontal gyrus2.62e-072
middle temporal gyrus3.33e-072


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)
MA0003.11.09804e-06
MA0004.10.221943
MA0006.10.112549
MA0007.10.599001
MA0009.10.621697
MA0014.10.000129423
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.664972
MA0042.10.608306
MA0043.10.621991
MA0046.10.611559
MA0048.10.0140676
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.157354
MA0056.10
MA0057.10.0128587
MA0058.10.153757
MA0059.10.15289
MA0060.10.0509127
MA0061.10.356644
MA0063.10
MA0066.10.818531
MA0067.10.924196
MA0068.10.111262
MA0069.10.607975
MA0070.10.597583
MA0071.10.746772
MA0072.10.593415
MA0073.10.0247836
MA0074.10.298586
MA0076.10.164578
MA0077.11.43229
MA0078.10.995054
MA0081.10.152999
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.0261898
MA0089.10
MA0090.10.997059
MA0091.11.19125
MA0092.10.570207
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.843378
MA0101.10.372085
MA0103.10.34743
MA0105.10.0516824
MA0106.10.33677
MA0107.10.551112
MA0108.21.18798
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.10.072201
MA0115.10.850405
MA0116.10.264652
MA0117.10.656858
MA0119.10.142224
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.11.56603
MA0136.10.30842
MA0139.10.0351037
MA0140.10.269307
MA0141.10.462123
MA0142.10.445733
MA0143.10.925263
MA0144.10.231909
MA0145.10.00588885
MA0146.17.9117e-05
MA0147.10.0784275
MA0148.10.240905
MA0149.10.261654
MA0062.20.0377014
MA0035.20.740647
MA0039.21.99256e-06
MA0138.20.38342
MA0002.20.174654
MA0137.20.398112
MA0104.20.0505812
MA0047.20.326636
MA0112.20.339585
MA0065.20.033787
MA0150.10.508545
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.10.0498326
MA0155.10.025611
MA0156.10.800227
MA0157.10.421609
MA0158.10
MA0159.10.270712
MA0160.10.703717
MA0161.10
MA0162.10.000394937
MA0163.10.000152387
MA0164.11.69021
MA0080.20.11444
MA0018.20.337929
MA0099.20.27482
MA0079.22.33512e-13
MA0102.21.14323
MA0258.11.24983
MA0259.10.0828875
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

No analysis results for this cluster

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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