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Coexpression cluster:C2539

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Full id: C2539_pineal_small_pituitary_parietal_melanoma_eye_diencephalon



Phase1 CAGE Peaks

Hg19::chr1:165414259..165414273,-p6@RXRG
Hg19::chr1:165414325..165414369,-p1@RXRG
Hg19::chr1:165414382..165414394,-p4@RXRG
Hg19::chr1:165414414..165414430,-p3@RXRG


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
adult organism6.70e-73114
neural tube1.71e-5356
neural rod1.71e-5356
future spinal cord1.71e-5356
neural keel1.71e-5356
regional part of nervous system2.51e-4953
regional part of brain2.51e-4953
neurectoderm1.09e-4486
neural plate4.83e-4482
presumptive neural plate4.83e-4482
central nervous system1.00e-4281
brain1.02e-4268
future brain1.02e-4268
regional part of forebrain8.87e-4241
forebrain8.87e-4241
anterior neural tube8.87e-4241
future forebrain8.87e-4241
nervous system3.15e-4089
ecto-epithelium1.77e-37104
pre-chordal neural plate3.01e-3361
telencephalon4.90e-3134
brain grey matter1.22e-3034
gray matter1.22e-3034
structure with developmental contribution from neural crest4.53e-30132
ectoderm-derived structure1.06e-29171
ectoderm1.06e-29171
presumptive ectoderm1.06e-29171
cerebral hemisphere1.64e-2832
regional part of telencephalon2.69e-2832
organ system subdivision3.98e-23223
regional part of cerebral cortex7.86e-2222
neocortex1.45e-2120
cerebral cortex1.34e-1825
pallium1.34e-1825
basal ganglion9.48e-159
nuclear complex of neuraxis9.48e-159
aggregate regional part of brain9.48e-159
collection of basal ganglia9.48e-159
cerebral subcortex9.48e-159
neural nucleus2.15e-149
nucleus of brain2.15e-149
anatomical cluster7.19e-14373
tube1.84e-13192
multi-tissue structure5.38e-13342
diencephalon1.09e-127
future diencephalon1.09e-127
posterior neural tube1.53e-1215
chordal neural plate1.53e-1215
anatomical conduit2.57e-12240
telencephalic nucleus4.25e-127
epithelium2.76e-11306
cell layer5.55e-11309
segmental subdivision of nervous system5.10e-1013
brainstem7.65e-106
organ part8.76e-10218
segmental subdivision of hindbrain7.63e-0912
hindbrain7.63e-0912
presumptive hindbrain7.63e-0912
organ8.45e-09503
gland of diencephalon2.28e-084
neuroendocrine gland2.28e-084
embryo2.37e-08592
temporal lobe2.41e-086
parietal lobe3.65e-085
corpus striatum4.11e-084
striatum4.11e-084
ventral part of telencephalon4.11e-084
future corpus striatum4.11e-084
regional part of diencephalon1.02e-074
germ layer2.69e-07560
germ layer / neural crest2.69e-07560
embryonic tissue2.69e-07560
presumptive structure2.69e-07560
germ layer / neural crest derived structure2.69e-07560
epiblast (generic)2.69e-07560
gyrus4.11e-076
embryonic structure4.64e-07564
developing anatomical structure8.05e-07581


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.12.82503
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.16.61141
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.12.85665
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.88496
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.20937
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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.