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{{Coexpression_clusters
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|full_id=C1851_salivary_submaxillary_parotid_small_pons_thyroid_throat
|id=C1851
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.07e-81!115;UBERON:0001049!9.62e-52!57;UBERON:0005068!9.62e-52!57;UBERON:0006241!9.62e-52!57;UBERON:0007135!9.62e-52!57;UBERON:0002616!9.07e-45!59;UBERON:0001017!9.55e-45!82;UBERON:0005743!1.28e-43!86;UBERON:0000955!6.67e-42!69;UBERON:0006238!6.67e-42!69;UBERON:0003075!1.71e-41!86;UBERON:0007284!1.71e-41!86;UBERON:0000073!3.19e-40!94;UBERON:0001016!3.19e-40!94;UBERON:0002346!4.67e-40!90;UBERON:0003080!6.73e-37!42;UBERON:0002780!4.17e-36!41;UBERON:0001890!4.17e-36!41;UBERON:0006240!4.17e-36!41;UBERON:0002020!6.53e-34!34;UBERON:0003528!6.53e-34!34;UBERON:0001893!1.03e-33!34;UBERON:0002791!1.96e-32!33;UBERON:0000153!3.13e-32!129;UBERON:0007811!3.13e-32!129;UBERON:0001869!3.55e-32!32;UBERON:0000033!9.71e-30!123;UBERON:0003056!1.88e-28!61;UBERON:0000956!4.00e-27!25;UBERON:0000203!4.00e-27!25;UBERON:0004121!8.09e-26!169;UBERON:0000924!1.80e-25!173;UBERON:0006601!1.80e-25!173;UBERON:0002619!4.01e-25!22;UBERON:0001950!3.74e-23!20;UBERON:0000477!1.37e-15!286;UBERON:0003076!1.61e-15!15;UBERON:0003057!1.61e-15!15;UBERON:0004111!1.51e-14!241;UBERON:0000481!3.80e-14!347;UBERON:0000025!3.97e-14!194;UBERON:0004732!2.55e-13!13;UBERON:0000062!2.80e-13!511;UBERON:0004733!1.69e-12!12;UBERON:0002028!1.69e-12!12;UBERON:0007277!1.69e-12!12;UBERON:0000064!3.24e-12!219;UBERON:0000475!6.42e-12!365;UBERON:0000483!7.74e-12!309;UBERON:0000119!1.73e-11!312;UBERON:0002298!4.58e-10!8;UBERON:0001871!3.69e-09!7;UBERON:0002680!4.17e-09!9;UBERON:0001895!4.17e-09!9;UBERON:0010092!4.17e-09!9;UBERON:0000468!5.91e-09!659;UBERON:0000922!1.03e-08!612;UBERON:0000467!1.23e-08!625;UBERON:0000200!1.38e-08!6;UBERON:0000480!1.46e-08!626;UBERON:0002308!2.91e-08!9;UBERON:0000125!2.91e-08!9;UBERON:0002050!3.22e-08!605;UBERON:0005423!3.22e-08!605;UBERON:0002420!5.97e-08!9;UBERON:0007245!5.97e-08!9;UBERON:0010009!5.97e-08!9;UBERON:0010011!5.97e-08!9;UBERON:0000454!5.97e-08!9;UBERON:0000923!7.14e-08!604;UBERON:0005291!7.14e-08!604;UBERON:0006598!7.14e-08!604;UBERON:0002532!7.14e-08!604;UBERON:0001872!4.90e-07!5;UBERON:0002021!8.04e-07!5
}}

Latest revision as of 11:53, 17 September 2013


Full id: C1851_salivary_submaxillary_parotid_small_pons_thyroid_throat



Phase1 CAGE Peaks

Hg19::chr1:217250308..217250349,-p9@ESRRG
Hg19::chr1:217251561..217251581,-p8@ESRRG
Hg19::chr1:217251585..217251611,-p11@ESRRG
Hg19::chr1:217251619..217251658,-p6@ESRRG
Hg19::chr1:217251670..217251682,-p19@ESRRG


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 organism1.04e-81114
neural tube1.23e-3756
neural rod1.23e-3756
future spinal cord1.23e-3756
neural keel1.23e-3756
regional part of nervous system1.72e-3553
regional part of brain1.72e-3553
neural plate5.64e-2982
presumptive neural plate5.64e-2982
central nervous system1.17e-2881
brain1.18e-2868
future brain1.18e-2868
neurectoderm4.49e-2786
nervous system1.17e-2489
regional part of forebrain3.01e-2441
forebrain3.01e-2441
anterior neural tube3.01e-2441
future forebrain3.01e-2441
brain grey matter6.98e-2434
gray matter6.98e-2434
telencephalon8.66e-2434
ecto-epithelium1.20e-21104
cerebral hemisphere2.12e-2132
structure with developmental contribution from neural crest2.12e-21132
organ system subdivision3.96e-21223
regional part of telencephalon4.36e-2132
ectoderm-derived structure7.68e-17171
ectoderm7.68e-17171
presumptive ectoderm7.68e-17171
pre-chordal neural plate7.82e-1761
regional part of cerebral cortex2.38e-1622
neocortex7.83e-1620
posterior neural tube9.30e-1515
chordal neural plate9.30e-1515
multi-tissue structure1.21e-14342
anatomical cluster3.71e-14373
cerebral cortex5.52e-1425
pallium5.52e-1425
segmental subdivision of hindbrain7.96e-1312
hindbrain7.96e-1312
presumptive hindbrain7.96e-1312
anatomical conduit8.05e-13240
neural nucleus1.96e-129
nucleus of brain1.96e-129
brainstem3.42e-126
gyrus5.70e-126
tube7.31e-12192
segmental subdivision of nervous system1.12e-1113
organ part3.00e-10218
organ6.85e-10503
telencephalic nucleus2.62e-097
basal ganglion2.72e-099
nuclear complex of neuraxis2.72e-099
aggregate regional part of brain2.72e-099
collection of basal ganglia2.72e-099
cerebral subcortex2.72e-099
corpus striatum1.90e-084
striatum1.90e-084
ventral part of telencephalon1.90e-084
future corpus striatum1.90e-084
regional part of metencephalon4.70e-089
metencephalon4.70e-089
future metencephalon4.70e-089
epithelium6.88e-08306
cell layer1.12e-07309
medulla oblongata6.35e-073
myelencephalon6.35e-073
future myelencephalon6.35e-073
pons6.48e-073
anatomical system7.63e-07624
anatomical group8.51e-07625


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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.11.8711
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.12.09554
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.22.01584
MA0018.20.781393
MA0099.20.699641
MA0079.23.83292e-05
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
FOXA1#316948.865135799508360.0003075468591372710.00316826656356653



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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