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|rna_box=103
|rna_box=103

Revision as of 16:52, 21 September 2012


Name:caudate nucleus - adult, donor10196
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecaudate nucleus
dev stageNA
sexfemale
age60
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0.275
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
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C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13802

Jaspar motifP-value
MA0002.20.044
MA0003.10.322
MA0004.10.292
MA0006.10.244
MA0007.10.471
MA0009.10.495
MA0014.10.722
MA0017.10.0186
MA0018.20.0768
MA0019.10.799
MA0024.10.754
MA0025.10.313
MA0027.10.95
MA0028.10.0505
MA0029.10.0331
MA0030.10.689
MA0031.10.806
MA0035.20.0348
MA0038.10.0644
MA0039.20.143
MA0040.10.846
MA0041.10.181
MA0042.10.501
MA0043.10.497
MA0046.10.0193
MA0047.20.0866
MA0048.10.0777
MA0050.10.00794
MA0051.10.044
MA0052.10.467
MA0055.10.00101
MA0057.10.978
MA0058.10.235
MA0059.10.0884
MA0060.10.485
MA0061.10.00706
MA0062.27.56069e-4
MA0065.20.00309
MA0066.10.0819
MA0067.10.485
MA0068.10.95
MA0069.10.676
MA0070.10.346
MA0071.10.0123
MA0072.10.4
MA0073.10.397
MA0074.10.211
MA0076.10.102
MA0077.10.0975
MA0078.10.794
MA0079.20.77
MA0080.21.16233e-8
MA0081.10.0247
MA0083.10.137
MA0084.10.239
MA0087.10.229
MA0088.10.144
MA0090.10.285
MA0091.10.165
MA0092.10.365
MA0093.10.318
MA0099.23.06842e-14
MA0100.10.769
MA0101.10.00538
MA0102.20.306
MA0103.10.161
MA0104.20.485
MA0105.10.00226
MA0106.10.00993
MA0107.10.00624
MA0108.20.553
MA0111.10.573
MA0112.20.00212
MA0113.10.673
MA0114.10.00896
MA0115.10.926
MA0116.10.00817
MA0117.10.752
MA0119.10.0991
MA0122.10.546
MA0124.10.92
MA0125.10.127
MA0131.10.743
MA0135.10.0349
MA0136.19.31511e-12
MA0137.20.0138
MA0138.20.416
MA0139.10.45
MA0140.10.0156
MA0141.10.0127
MA0142.10.484
MA0143.10.155
MA0144.10.806
MA0145.10.176
MA0146.10.0055
MA0147.10.372
MA0148.10.0725
MA0149.10.0197
MA0150.15.78916e-4
MA0152.10.783
MA0153.10.605
MA0154.10.0477
MA0155.10.607
MA0156.12.30649e-8
MA0157.10.44
MA0159.10.0393
MA0160.10.0299
MA0162.10.137
MA0163.17.74292e-6
MA0164.10.687
MA0258.10.0315
MA0259.10.848



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13802

Novel motifP-value
10.0585
100.0364
1000.235
1010.409
1020.927
1030.0909
1040.0488
1050.111
1060.031
1070.125
1080.9
1090.00442
110.0107
1100.0736
1110.247
1120.615
1130.336
1140.232
1150.947
1160.0773
1170.0077
1180.17
1190.223
120.636
1200.183
1210.253
1220.74
1230.477
1240.0745
1250.524
1260.0565
1270.592
1280.236
1290.699
130.00148
1300.428
1310.0332
1320.648
1330.00311
1340.751
1350.0789
1360.00201
1370.899
1380.841
1390.399
140.763
1400.558
1410.607
1420.601
1430.0882
1440.958
1450.142
1460.4
1470.92
1480.348
1490.46
150.0727
1500.137
1510.548
1520.0571
1530.89
1540.569
1550.576
1560.648
1570.493
1580.505
1590.0762
160.0506
1600.26
1610.485
1620.724
1630.787
1640.00818
1650.221
1660.785
1670.636
1680.345
1690.00891
170.141
180.0956
190.188
20.878
200.0833
210.0531
220.157
230.604
240.0702
250.433
261.68759e-4
270.933
280.866
290.0121
30.0327
300.648
310.893
320.0081
330.0594
340.645
350.668
360.193
370.0253
380.364
390.387
40.83
400.0552
410.468
420.247
430.106
440.248
450.714
460.0535
470.0701
480.0437
490.18
50.621
500.259
510.457
520.592
530.953
540.397
550.555
560.486
570.221
580.373
590.0621
60.938
600.0667
610.123
620.279
630.173
640.151
650.278
660.131
670.339
680.18
690.419
70.0716
700.0303
710.0107
720.566
730.0243
740.463
750.0156
760.331
770.175
782.13406e-4
790.259
80.0699
800.932
810.516
820.592
830.0735
840.526
850.256
860.115
872.80306e-4
880.538
890.55
90.5
900.0967
910.526
920.557
930.628
940.161
950.0201
960.971
970.7
980.2
990.502



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs13802


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000955 (brain)
0001873 (caudate nucleus)
0000369 (corpus striatum)
0002435 (striatum)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009663 (telencephalic nucleus)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0000125 (neural nucleus)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0002308 (nucleus of brain)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0005383 (caudate-putamen)
0010011 (collection of basal ganglia)
0000204 (ventral part of telencephalon)
0005382 (dorsal striatum)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0010164 (human caudate nucleus - adult donor sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010122 (future caudate nucleus)
UBERON:0010316 (germ layer / neural crest)

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