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Coexpression cluster:C2284: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,1.75588,0.534346,0.739643,0.821651,0.395818,1.01802,0.902371,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.806311,0.682839,1.09415,0.433165,0.344471,1.23824,3.353,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,2.26333,0.0946706,0.61613,0.822818,0.694903,2.24703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,1.15724,2.51889,1.15558,0.939507,0.272395,4.11867,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,1.22649,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,1.75588,0.534346,0.739643,0.821651,0.395818,1.01802,0.902371,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.806311,0.682839,1.09415,0.433165,0.344471,1.23824,3.353,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,2.26333,0.0946706,0.61613,0.822818,0.694903,2.24703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,1.15724,2.51889,1.15558,0.939507,0.272395,4.11867,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,1.22649,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;1.35734,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;1.66718,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;1.28333,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;1.8408,MA0072.1;1.1744,MA0073.1;0.599068,MA0074.1;0.819248,MA0076.1;1.51122,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;2.4958,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;1.83323,MA0039.2;0.10559,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.577908,MA0150.1;2.59564,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.02191,MA0156.1;0.560797,MA0157.1;2.23474,MA0158.1;0,MA0159.1;3.02177,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.122011,MA0102.2;1.75932,MA0258.1;1.88931,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:32, 22 January 2013


Full id: C2284_occipital_brain_hippocampus_medial_medulla_amygdala_cerebellum



Phase1 CAGE Peaks

Hg19::chr14:21490590..21490616,-p8@NDRG2
Hg19::chr14:21490622..21490648,-p9@NDRG2
Hg19::chr14:21490653..21490665,-p14@NDRG2
Hg19::chr3:121613362..121613373,+p4@SLC15A2


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:0015334high affinity oligopeptide transporter activity0.00204086638570241
GO:0022897proton-dependent peptide secondary active transmembrane transporter activity0.00204086638570241
GO:0015333peptide:hydrogen symporter activity0.00204086638570241
GO:0015295solute:hydrogen symporter activity0.00306120946214148
GO:0015198oligopeptide transporter activity0.00367334321487522
GO:0015197peptide transporter activity0.00408137230575627
GO:0006857oligopeptide transport0.00650382537410799
GO:0015893drug transport0.00650382537410799
GO:0015833peptide transport0.0132584071746926
GO:0042493response to drug0.0192688714762954
GO:0015294solute:cation symporter activity0.0316738953436382



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 organism3.54e-106114
neural tube4.00e-5856
neural rod4.00e-5856
future spinal cord4.00e-5856
neural keel4.00e-5856
regional part of nervous system1.45e-5353
regional part of brain1.45e-5353
central nervous system2.95e-4281
brain3.81e-4268
future brain3.81e-4268
neural plate1.46e-4182
presumptive neural plate1.46e-4182
regional part of forebrain1.73e-4141
forebrain1.73e-4141
anterior neural tube1.73e-4141
future forebrain1.73e-4141
neurectoderm7.76e-3986
nervous system3.80e-3889
brain grey matter1.30e-3734
gray matter1.30e-3734
telencephalon2.88e-3734
cerebral hemisphere1.37e-3432
regional part of telencephalon1.39e-3432
ecto-epithelium1.13e-30104
structure with developmental contribution from neural crest7.01e-30132
regional part of cerebral cortex7.12e-2922
pre-chordal neural plate1.93e-2761
neocortex9.96e-2620
cerebral cortex1.06e-2425
pallium1.06e-2425
organ system subdivision1.67e-24223
ectoderm-derived structure1.00e-22171
ectoderm1.00e-22171
presumptive ectoderm1.00e-22171
posterior neural tube3.58e-1715
chordal neural plate3.58e-1715
anatomical conduit4.38e-17240
tube3.98e-16192
organ3.68e-15503
anatomical cluster5.96e-15373
basal ganglion1.07e-149
nuclear complex of neuraxis1.07e-149
aggregate regional part of brain1.07e-149
collection of basal ganglia1.07e-149
cerebral subcortex1.07e-149
neural nucleus1.11e-149
nucleus of brain1.11e-149
segmental subdivision of nervous system3.23e-1413
multi-tissue structure5.78e-14342
segmental subdivision of hindbrain6.88e-1312
hindbrain6.88e-1312
presumptive hindbrain6.88e-1312
telencephalic nucleus1.18e-117
organ part6.14e-11218
brainstem1.63e-106
gyrus2.62e-106
embryo6.23e-10592
embryonic structure7.31e-10564
developing anatomical structure1.21e-09581
germ layer1.22e-09560
germ layer / neural crest1.22e-09560
embryonic tissue1.22e-09560
presumptive structure1.22e-09560
germ layer / neural crest derived structure1.22e-09560
epiblast (generic)1.22e-09560
multi-cellular organism2.11e-09656
occipital lobe4.04e-095
limbic system4.31e-095
anatomical system8.55e-09624
anatomical group9.87e-09625
regional part of metencephalon1.27e-089
metencephalon1.27e-089
future metencephalon1.27e-089
parietal lobe1.70e-085
epithelium5.53e-08306
cell layer9.61e-08309
corpus striatum2.97e-074
striatum2.97e-074
ventral part of telencephalon2.97e-074
future corpus striatum2.97e-074
regional part of diencephalon6.66e-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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0048.10.25531
MA0050.11.66718
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.28333
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
MA0071.11.8408
MA0072.11.1744
MA0073.10.599068
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
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
MA0141.12.4958
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
MA0035.21.83323
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.12.59564
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.12.23474
MA0158.10
MA0159.13.02177
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
MA0102.21.75932
MA0258.11.88931
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.

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