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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:39, 17 September 2013


Full id: C1198_Neural_parietal_occipital_Astrocyte_brain_duodenum_temporal



Phase1 CAGE Peaks

Hg19::chr14:29234581..29234601,+p2@FOXG1
Hg19::chr3:13083919..13083940,-p@chr3:13083919..13083940
-
Hg19::chr3:26664291..26664329,+p1@LRRC3B
Hg19::chr6:118228389..118228435,+p1@SLC35F1
Hg19::chr8:28351707..28351781,+p1@FZD3
Hg19::chr9:126774018..126774055,+p1@LHX2
Hg19::chr9:126774058..126774081,+p3@LHX2


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

GO IDGO nameFDR corrected p-value
GO:0007399nervous system development0.00857355975151682
GO:0007420brain development0.00857355975151682
GO:0048513organ development0.012219673955238
GO:0007417central nervous system development0.012219673955238
GO:0001736establishment of planar polarity0.0133886523705115
GO:0001738morphogenesis of a polarized epithelium0.0133886523705115
GO:0048731system development0.0133886523705115
GO:0007164establishment of tissue polarity0.0133886523705115
GO:0042813Wnt receptor activity0.013600369910269
GO:0001843neural tube closure0.0152905103453416
GO:0014020primary neural tube formation0.0152905103453416
GO:0048856anatomical structure development0.0152905103453416
GO:0004926non-G-protein coupled 7TM receptor activity0.0152905103453416
GO:0001839neural plate morphogenesis0.0152905103453416
GO:0001841neural tube formation0.0152905103453416
GO:0001840neural plate development0.0152905103453416
GO:0001838embryonic epithelial tube formation0.0152905103453416
GO:0007275multicellular organismal development0.0152905103453416
GO:0021915neural tube development0.0152905103453416
GO:0016331morphogenesis of embryonic epithelium0.0168165908635914
GO:0042472inner ear morphogenesis0.0194503404689869
GO:0009953dorsal/ventral pattern formation0.0194503404689869
GO:0042471ear morphogenesis0.0205943935320225
GO:0048839inner ear development0.0241829077621319
GO:0043583ear development0.0248812194198963
GO:0043565sequence-specific DNA binding0.0248812194198963
GO:0007498mesoderm development0.0248812194198963
GO:0032502developmental process0.0304572556182887
GO:0002009morphogenesis of an epithelium0.0331313768523156
GO:0032501multicellular organismal process0.038969389921935
GO:0035239tube morphogenesis0.038969389921935
GO:0045177apical part of cell0.038969389921935
GO:0007423sensory organ development0.038969389921935
GO:0003002regionalization0.038969389921935
GO:0048598embryonic morphogenesis0.0390841434722103
GO:0009792embryonic development ending in birth or egg hatching0.0390841434722103
GO:0043009chordate embryonic development0.0390841434722103
GO:0035295tube development0.0468078249567275
GO:0003700transcription factor activity0.0471084598502684
GO:0007389pattern specification process0.0471084598502684



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
neural cell1.81e-0925
embryonic stem cell9.40e-085
astrocyte of the cerebral cortex7.23e-073
neurectodermal cell9.23e-0759
Uber Anatomy
Ontology termp-valuen
central nervous system6.52e-6881
neural tube6.51e-6656
neural rod6.51e-6656
future spinal cord6.51e-6656
neural keel6.51e-6656
nervous system1.23e-6589
regional part of nervous system7.24e-6553
regional part of brain7.24e-6553
neural plate5.38e-6182
presumptive neural plate5.38e-6182
brain1.77e-5868
future brain1.77e-5868
neurectoderm2.81e-5786
regional part of forebrain4.19e-5541
forebrain4.19e-5541
anterior neural tube4.19e-5541
future forebrain4.19e-5541
telencephalon1.74e-5434
brain grey matter5.94e-5434
gray matter5.94e-5434
pre-chordal neural plate4.69e-5361
cerebral hemisphere9.92e-5232
regional part of telencephalon2.45e-5132
ecto-epithelium1.44e-47104
ectoderm-derived structure7.22e-41171
ectoderm7.22e-41171
presumptive ectoderm7.22e-41171
cerebral cortex1.53e-4025
pallium1.53e-4025
structure with developmental contribution from neural crest3.23e-40132
regional part of cerebral cortex3.00e-3522
neocortex6.91e-3220
adult organism2.10e-28114
organ system subdivision2.37e-26223
anatomical cluster2.72e-18373
basal ganglion2.26e-159
nuclear complex of neuraxis2.26e-159
aggregate regional part of brain2.26e-159
collection of basal ganglia2.26e-159
cerebral subcortex2.26e-159
organ part1.13e-14218
neural nucleus1.42e-149
nucleus of brain1.42e-149
tube6.23e-13192
posterior neural tube3.58e-1215
chordal neural plate3.58e-1215
telencephalic nucleus4.36e-127
gyrus3.06e-116
epithelium3.92e-11306
segmental subdivision of hindbrain5.46e-1112
hindbrain5.46e-1112
presumptive hindbrain5.46e-1112
cell layer7.65e-11309
segmental subdivision of nervous system5.67e-1013
multi-tissue structure6.22e-10342
limbic system7.15e-105
regional part of metencephalon7.97e-109
metencephalon7.97e-109
future metencephalon7.97e-109
temporal lobe1.00e-096
occipital lobe1.19e-095
embryo1.71e-09592
parietal lobe2.08e-095
pigment epithelium of eye1.58e-0811
anatomical conduit2.06e-08240
corpus striatum4.37e-084
striatum4.37e-084
ventral part of telencephalon4.37e-084
future corpus striatum4.37e-084
multi-cellular organism3.91e-07656
organ7.27e-07503
developing anatomical structure7.88e-07581
atypical epithelium8.20e-074


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)
MA0003.13.37926
MA0004.10.502801
MA0006.10.904424
MA0007.10.483857
MA0009.10.973289
MA0014.10.0723474
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.649431
MA0056.10
MA0057.10.744639
MA0058.10.406232
MA0059.10.404929
MA0060.10.638423
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.00958848
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.695228
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.581146
MA0146.10.547931
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.0553061
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.636673
MA0047.20.636643
MA0112.20.0758925
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.11.13451
MA0155.10.910701
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.11.13878
MA0163.10.632664
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.23.31082
MA0102.21.51913
MA0258.10.245543
MA0259.11.43531
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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