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Coexpression cluster:C1667: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;3.78382,MA0004.1;1.51734,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.660087,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.288856,MA0056.1;0,MA0057.1;0.554727,MA0058.1;2.23895,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;1.44118,MA0063.1;0,MA0066.1;1.74614,MA0067.1;1.43651,MA0068.1;1.98392,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.00220137,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;1.92154,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;2.01552,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;2.02769,MA0103.1;0.442769,MA0105.1;0.520776,MA0106.1;1.83541,MA0107.1;1.74965,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;1.82062,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.527987,MA0138.2;0.837782,MA0002.2;0.83106,MA0137.2;1.20193,MA0104.2;0.858845,MA0047.2;0.767096,MA0112.2;1.96224,MA0065.2;0.449243,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;1.3196,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;1.77901,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;0.680296,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;2.44686,MA0102.2;1.66336,MA0258.1;1.63655,MA0259.1;1.02361,MA0442.1;0
}}
}}

Revision as of 20:05, 22 January 2013


Full id: C1667_corpus_diaphragm_globus_tongue_diencephalon_optic_thalamus



Phase1 CAGE Peaks

Hg19::chr12:21680455..21680478,+p2@C12orf39
Hg19::chr12:21680481..21680499,+p7@C12orf39
Hg19::chr14:35183743..35183754,-p9@CFL2
Hg19::chr14:35183755..35183770,-p7@CFL2
Hg19::chr1:201857798..201857813,+p2@SHISA4


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 organism2.91e-29114
structure with developmental contribution from neural crest2.16e-27132
neural tube2.40e-2556
neural rod2.40e-2556
future spinal cord2.40e-2556
neural keel2.40e-2556
neural plate1.41e-2482
presumptive neural plate1.41e-2482
multi-tissue structure6.56e-24342
nervous system1.31e-2389
regional part of nervous system1.32e-2353
regional part of brain1.32e-2353
central nervous system7.25e-2381
brain7.94e-2268
future brain7.94e-2268
neurectoderm1.01e-2186
anatomical cluster2.27e-20373
ectoderm-derived structure7.36e-19171
ectoderm7.36e-19171
presumptive ectoderm7.36e-19171
ecto-epithelium1.20e-18104
regional part of forebrain1.22e-1841
forebrain1.22e-1841
anterior neural tube1.22e-1841
future forebrain1.22e-1841
cell layer5.54e-18309
epithelium9.41e-18306
pre-chordal neural plate1.77e-1661
brain grey matter1.87e-1634
gray matter1.87e-1634
telencephalon1.90e-1634
regional part of telencephalon3.52e-1532
cerebral hemisphere4.20e-1532
anatomical conduit1.99e-14240
organ system subdivision2.61e-14223
tube9.03e-14192
multi-cellular organism5.40e-13656
anatomical system3.32e-12624
anatomical group6.32e-12625
regional part of cerebral cortex1.35e-1122
cerebral cortex6.42e-1125
pallium6.42e-1125
neocortex2.54e-1020
mesenchyme8.76e-09160
entire embryonic mesenchyme8.76e-09160
organ part1.26e-08218
posterior neural tube6.80e-0815
chordal neural plate6.80e-0815
organ7.04e-08503
organism subdivision8.68e-08264
dense mesenchyme tissue1.08e-0773
embryo1.55e-07592
paraxial mesoderm2.11e-0772
presumptive paraxial mesoderm2.11e-0772
neural nucleus2.81e-079
nucleus of brain2.81e-079
basal ganglion3.69e-079
nuclear complex of neuraxis3.69e-079
aggregate regional part of brain3.69e-079
collection of basal ganglia3.69e-079
cerebral subcortex3.69e-079
developing anatomical structure4.23e-07581
somite4.98e-0771
presomitic mesoderm4.98e-0771
presumptive segmental plate4.98e-0771
dermomyotome4.98e-0771
trunk paraxial mesoderm4.98e-0771
segmental subdivision of nervous system6.88e-0713


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)
MA0003.13.78382
MA0004.11.51734
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
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
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.554727
MA0058.12.23895
MA0059.10.522232
MA0060.10.321781
MA0061.11.44118
MA0063.10
MA0066.11.74614
MA0067.11.43651
MA0068.11.98392
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.92154
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.12.01552
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.12.02769
MA0103.10.442769
MA0105.10.520776
MA0106.11.83541
MA0107.11.74965
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
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
MA0145.10.442008
MA0146.11.82062
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.527987
MA0138.20.837782
MA0002.20.83106
MA0137.21.20193
MA0104.20.858845
MA0047.20.767096
MA0112.21.96224
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.3196
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.77901
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.22.44686
MA0102.21.66336
MA0258.11.63655
MA0259.11.02361
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
BHLHE40#8553217.9487254187910.004747812859838950.022317797608638
HNF4G#3174211.50136901057870.01127438304921050.0413718875400194
NANOG#79923211.69791139240510.01091164951956080.0402146151518601



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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