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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 11:16, 17 September 2013


Full id: C298_small_optic_substantia_thalamus_diencephalon_globus_occipital



Phase1 CAGE Peaks

Hg19::chr10:71333172..71333186,-p1@NEUROG3
Hg19::chr12:7401767..7401780,+p@chr12:7401767..7401780
+
Hg19::chr13:112626645..112626656,+p@chr13:112626645..112626656
+
Hg19::chr13:112626665..112626679,+p@chr13:112626665..112626679
+
Hg19::chr13:25685542..25685552,+p@chr13:25685542..25685552
+
Hg19::chr15:92459161..92459167,+p@chr15:92459161..92459167
+
Hg19::chr15:92459244..92459268,+p@chr15:92459244..92459268
+
Hg19::chr15:92459275..92459283,+p@chr15:92459275..92459283
+
Hg19::chr15:92459318..92459327,+p@chr15:92459318..92459327
+
Hg19::chr15:92459332..92459338,+p@chr15:92459332..92459338
+
Hg19::chr16:34378161..34378168,+p@chr16:34378161..34378168
+
Hg19::chr16:85617478..85617492,-p@chr16:85617478..85617492
-
Hg19::chr19:38423014..38423072,+p3@SIPA1L3
Hg19::chr1:40367530..40367597,-p1@MYCL1
Hg19::chr1:40367668..40367684,-p2@MYCL1
Hg19::chr1:40367692..40367703,-p3@MYCL1
Hg19::chr20:21378152..21378169,-p1@NKX2-4
Hg19::chr20:22449463..22449467,-p@chr20:22449463..22449467
-
Hg19::chr21:43733727..43733736,-p8@TFF3
Hg19::chr22:27044125..27044132,-p@chr22:27044125..27044132
-
Hg19::chr22:44569007..44569025,+p8@PARVG
Hg19::chr22:44569031..44569036,+p27@PARVG
Hg19::chr22:47425875..47425879,-p@chr22:47425875..47425879
-
Hg19::chr3:140947563..140947577,+p14@ACPL2
Hg19::chr3:180892810..180892816,+p23@SOX2-OT
Hg19::chr3:180892844..180892856,+p13@SOX2-OT
Hg19::chr3:180892861..180892862,+p31@SOX2-OT
Hg19::chr3:180892876..180892890,+p11@SOX2-OT
Hg19::chr3:181414213..181414253,+p@chr3:181414213..181414253
+
Hg19::chr3:181417231..181417239,+p12@SOX2-OT
Hg19::chr3:181417241..181417256,+p3@SOX2-OT
Hg19::chr3:181417264..181417270,+p7@SOX2-OT
Hg19::chr3:181417276..181417285,+p8@SOX2-OT
Hg19::chr3:181417560..181417569,-p@chr3:181417560..181417569
-
Hg19::chr3:181432833..181432842,+p@chr3:181432833..181432842
+
Hg19::chr3:181459149..181459161,+p@chr3:181459149..181459161
+
Hg19::chr3:181459204..181459208,+p@chr3:181459204..181459208
+
Hg19::chr3:19189765..19189793,+p2@KCNH8
Hg19::chr4:163124750..163124764,-p@chr4:163124750..163124764
-
Hg19::chr5:15516888..15516924,+p@chr5:15516888..15516924
+
Hg19::chr8:53163002..53163004,-p@chr8:53163002..53163004
-
Hg19::chr9:117670443..117670445,-p@chr9:117670443..117670445
-


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>disease_data<br>

Cell Type
Ontology termp-valuen
Merkel cell1.33e-152
keratinocyte5.08e-075
Uber Anatomy
Ontology termp-valuen
nucleus accumbens2.37e-291
ventral striatum2.37e-291
insula4.20e-291
medulla oblongata1.09e-103
myelencephalon1.09e-103
future myelencephalon1.09e-103
regional part of nervous system7.74e-0953
regional part of brain7.74e-0953
regional part of telencephalon2.12e-0832
cerebral hemisphere2.12e-0832
neural tube2.14e-0856
neural rod2.14e-0856
future spinal cord2.14e-0856
neural keel2.14e-0856
corpus striatum2.26e-084
striatum2.26e-084
ventral part of telencephalon2.26e-084
future corpus striatum2.26e-084
brain grey matter5.87e-0834
gray matter5.87e-0834
telencephalon5.87e-0834
ecto-epithelium4.92e-07104
limbic system6.04e-075
brain6.53e-0768
future brain6.53e-0768
regional part of forebrain9.81e-0741
forebrain9.81e-0741
anterior neural tube9.81e-0741
future forebrain9.81e-0741
Disease
Ontology termp-valuen
lung small cell carcinoma2.11e-084
cervical cancer4.79e-075


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)
MA0003.10.00437356
MA0004.10.404373
MA0006.10.305199
MA0007.10.660504
MA0009.10.309236
MA0014.10.0724043
MA0017.10.0796459
MA0019.10.351488
MA0024.10.234026
MA0025.10.413966
MA0027.11.81465
MA0028.10.17175
MA0029.10.24734
MA0030.10.23941
MA0031.10.196546
MA0038.10.0872867
MA0040.12.002
MA0041.12.18132
MA0042.10.0434862
MA0043.10.309473
MA0046.10.301098
MA0048.10.319872
MA0050.11.48865
MA0051.10.289167
MA0052.10.254136
MA0055.10.541802
MA0056.10
MA0057.10.423246
MA0058.10.737495
MA0059.10.732879
MA0060.10.198625
MA0061.10.253661
MA0063.10
MA0066.10.294839
MA0067.10.570397
MA0068.10.397844
MA0069.10.298233
MA0070.10.289965
MA0071.10.248466
MA0072.10.286664
MA0073.13.76232e-07
MA0074.10.0850822
MA0076.10.109351
MA0077.12.99473
MA0078.10.418758
MA0081.10.0964507
MA0083.10.314889
MA0084.10.739331
MA0087.12.17369
MA0088.10.102777
MA0089.10
MA0090.10.0292582
MA0091.10.721662
MA0092.10.340194
MA0093.10.528268
MA0095.10
MA0098.10
MA0100.10.0935814
MA0101.10.15919
MA0103.11.41956
MA0105.10.238866
MA0106.10.106627
MA0107.10.0796014
MA0108.20.194591
MA0109.10
MA0111.10.899363
MA0113.10.114834
MA0114.10.0751572
MA0115.10.50405
MA0116.10.0827104
MA0117.10.337847
MA0119.10.0849363
MA0122.10.357986
MA0124.10.468805
MA0125.10.399431
MA0130.10
MA0131.10.144593
MA0132.10
MA0133.10
MA0135.10.332279
MA0136.10.0904607
MA0139.10.0581541
MA0140.10.245432
MA0141.10.0950609
MA0142.11.00524
MA0143.10.368245
MA0144.10.063455
MA0145.10.133912
MA0146.10.00233561
MA0147.11.08415
MA0148.10.787347
MA0149.10.234527
MA0062.20.00670702
MA0035.21.34707
MA0039.20.0135126
MA0138.20.420466
MA0002.20.087342
MA0137.20.0690027
MA0104.20.992126
MA0047.20.677402
MA0112.20.269149
MA0065.20.022429
MA0150.10.116147
MA0151.10
MA0152.10.539107
MA0153.10.385866
MA0154.11.02982
MA0155.10.2389
MA0156.10.0704039
MA0157.10.160178
MA0158.10
MA0159.10.00516027
MA0160.10.482489
MA0161.10
MA0162.10.0336195
MA0163.10.721272
MA0164.10.384671
MA0080.20.311926
MA0018.20.107308
MA0099.20.072601
MA0079.20.00145279
MA0102.20.773745
MA0258.10.408158
MA0259.10.572972
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

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