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Coexpression cluster:C1027: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0151272,0.341646,0.481684,1.48054,0.480078,0.554663,0.561282,0.190005,0.0394821,0.450635,0.597407,0.152895,0.543352,0.81316,0.322799,0.774423,0.698835,0.163559,0.0766963,0.341703,0.405031,0.472508,0.805193,0.385586,0.619829,0.135503,0.470396,0.304828,0.388322,0.429397,0.810962,0.220667,0.154814,0.269459,0.0137136,0.266487,0.481208,0.685417,0.174436,0.268162,0.413601,0.0547276,0.299183,0.0169887,0.371118,0.555735,0.440085,0.0498256,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,0.513089,0.85167,0.558065,0.556977,0.746929,0.575742,0.712797,2.54508,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,0.138565,0.401476,0.730167,0.797419,0.989108,0.96869,0.745864,1.40937,0.19474,0.986227,0.0958904,0.26222,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.644398,0.302606,0.239285,0.488357,0.87,0.664183,0.106284,1.27523,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.116216,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,1.35238,0.83262,1.07171,0.674618,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,1.05631,0.224241,0.283443,0.0510299,0.960402,0.183004,1.37178,1.36372,0.643609,0.288769,1.00225,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.611402,0.553354,0.146591
|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0151272,0.341646,0.481684,1.48054,0.480078,0.554663,0.561282,0.190005,0.0394821,0.450635,0.597407,0.152895,0.543352,0.81316,0.322799,0.774423,0.698835,0.163559,0.0766963,0.341703,0.405031,0.472508,0.805193,0.385586,0.619829,0.135503,0.470396,0.304828,0.388322,0.429397,0.810962,0.220667,0.154814,0.269459,0.0137136,0.266487,0.481208,0.685417,0.174436,0.268162,0.413601,0.0547276,0.299183,0.0169887,0.371118,0.555735,0.440085,0.0498256,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,0.513089,0.85167,0.558065,0.556977,0.746929,0.575742,0.712797,2.54508,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,0.138565,0.401476,0.730167,0.797419,0.989108,0.96869,0.745864,1.40937,0.19474,0.986227,0.0958904,0.26222,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.644398,0.302606,0.239285,0.488357,0.87,0.664183,0.106284,1.27523,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.116216,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,1.35238,0.83262,1.07171,0.674618,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,1.05631,0.224241,0.283443,0.0510299,0.960402,0.183004,1.37178,1.36372,0.643609,0.288769,1.00225,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.611402,0.553354,0.146591
|tfbs_overrepresentation_jaspar=MA0003.1;0.140538,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.00962431,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.0955945,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.283474,MA0056.1;0,MA0057.1;0.0912556,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.497495,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.000871324,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.054222,MA0089.1;0,MA0090.1;1.01596,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.0818021,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.155155,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;1.17059,MA0145.1;0.220937,MA0146.1;0.00761723,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.00915579,MA0138.2;0.653421,MA0002.2;1.61227,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;0.0572179,MA0065.2;0.0631316,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.577214,MA0155.1;0.0535085,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.0163939,MA0163.1;0.0517199,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;2.25601e-06,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0
}}
}}

Revision as of 19:38, 22 January 2013


Full id: C1027_hippocampus_occipital_optic_globus_thalamus_cerebral_locus



Phase1 CAGE Peaks

Hg19::chr13:66878571..66878580,-p@chr13:66878571..66878580
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Hg19::chr13:98045526..98045628,+p@chr13:98045526..98045628
+
Hg19::chr1:109856117..109856176,-p@chr1:109856117..109856176
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Hg19::chr1:109856200..109856211,-p@chr1:109856200..109856211
-
Hg19::chr1:155851487..155851498,+p@chr1:155851487..155851498
+
Hg19::chr3:58551136..58551152,-p@chr3:58551136..58551152
-
Hg19::chrX:13789494..13789511,-p@chrX:13789494..13789511
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Hg19::chrX:13789649..13789660,-p@chrX:13789649..13789660
-


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
neural tube5.69e-8256
neural rod5.69e-8256
future spinal cord5.69e-8256
neural keel5.69e-8256
regional part of nervous system1.39e-7553
regional part of brain1.39e-7553
central nervous system3.42e-6781
neural plate7.98e-6782
presumptive neural plate7.98e-6782
regional part of forebrain1.73e-6641
forebrain1.73e-6641
anterior neural tube1.73e-6641
future forebrain1.73e-6641
brain2.08e-6368
future brain2.08e-6368
neurectoderm5.59e-6386
adult organism1.54e-62114
nervous system1.05e-6189
brain grey matter2.55e-6134
gray matter2.55e-6134
telencephalon2.10e-6034
regional part of telencephalon4.90e-5732
cerebral hemisphere1.07e-5632
ecto-epithelium2.89e-53104
pre-chordal neural plate1.39e-4861
structure with developmental contribution from neural crest1.51e-43132
cerebral cortex7.94e-4325
pallium7.94e-4325
regional part of cerebral cortex5.29e-3822
neocortex1.17e-3320
ectoderm-derived structure1.48e-33171
ectoderm1.48e-33171
presumptive ectoderm1.48e-33171
tube2.09e-24192
organ system subdivision1.82e-23223
neural nucleus1.04e-199
nucleus of brain1.04e-199
basal ganglion1.29e-199
nuclear complex of neuraxis1.29e-199
aggregate regional part of brain1.29e-199
collection of basal ganglia1.29e-199
cerebral subcortex1.29e-199
anatomical conduit7.13e-19240
epithelium2.07e-17306
cell layer4.61e-17309
anatomical cluster1.31e-16373
posterior neural tube2.80e-1615
chordal neural plate2.80e-1615
telencephalic nucleus1.45e-157
multi-tissue structure3.20e-14342
brainstem2.11e-136
gyrus7.64e-136
segmental subdivision of nervous system1.02e-1213
limbic system8.05e-125
organ part9.64e-12218
occipital lobe2.80e-115
temporal lobe3.33e-116
segmental subdivision of hindbrain7.45e-1112
hindbrain7.45e-1112
presumptive hindbrain7.45e-1112
corpus striatum2.57e-094
striatum2.57e-094
ventral part of telencephalon2.57e-094
future corpus striatum2.57e-094
regional part of diencephalon3.24e-094
organ3.60e-08503
diencephalon6.86e-087
future diencephalon6.86e-087
spinal cord8.28e-083
dorsal region element8.28e-083
dorsum8.28e-083
pons1.26e-073
caudate-putamen1.31e-073
dorsal striatum1.31e-073
medulla oblongata1.94e-073
myelencephalon1.94e-073
future myelencephalon1.94e-073
frontal cortex2.20e-073
parietal lobe3.39e-075
valve3.91e-073
cardiac mesenchyme3.91e-073
cardial valve3.91e-073
tunica intima3.91e-073
heart layer3.91e-073
endocardium3.91e-073
endocardial cushion3.91e-073
presumptive endocardium3.91e-073
embryo4.16e-07592
embryonic structure5.05e-07564
male genital duct5.45e-073
internal male genitalia5.45e-073


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)
MA0003.10.140538
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.000871324
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.11.01596
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.11.17059
MA0145.10.220937
MA0146.10.00761723
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.00915579
MA0138.20.653421
MA0002.21.61227
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0517199
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.22.25601e-06
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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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