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FF:10158-103A5: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:15, 29 March 2012


Name:substantia nigra, adult, donor10252
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesubstantia nigra
dev stageNA
sexfemale
age76
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-Neural0.0582
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.838
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.00209
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.3
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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 no result for this sample


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: CNhs12318

Jaspar motifP-value
MA0002.20.0601
MA0003.10.145
MA0004.10.375
MA0006.10.445
MA0007.10.76
MA0009.10.171
MA0014.10.801
MA0017.10.00623
MA0018.20.831
MA0019.10.835
MA0024.10.61
MA0025.10.0894
MA0027.10.715
MA0028.10.0654
MA0029.10.0725
MA0030.10.072
MA0031.10.0106
MA0035.20.0267
MA0038.10.47
MA0039.20.207
MA0040.10.863
MA0041.10.38
MA0042.10.774
MA0043.10.585
MA0046.10.00113
MA0047.20.897
MA0048.10.196
MA0050.10.159
MA0051.10.18
MA0052.10.24
MA0055.10.0047
MA0057.10.76
MA0058.10.609
MA0059.10.152
MA0060.10.605
MA0061.17.10675e-4
MA0062.20.00275
MA0065.20.00385
MA0066.10.0108
MA0067.10.703
MA0068.10.949
MA0069.10.987
MA0070.10.687
MA0071.10.0302
MA0072.10.389
MA0073.10.606
MA0074.10.258
MA0076.10.116
MA0077.16.31101e-4
MA0078.10.535
MA0079.20.799
MA0080.24.69804e-5
MA0081.10.0315
MA0083.10.0102
MA0084.10.0755
MA0087.10.33
MA0088.10.654
MA0090.10.259
MA0091.10.752
MA0092.10.215
MA0093.10.479
MA0099.23.65352e-25
MA0100.10.392
MA0101.13.92553e-4
MA0102.20.323
MA0103.10.0153
MA0104.20.438
MA0105.13.56372e-5
MA0106.10.0217
MA0107.11.60214e-4
MA0108.20.0578
MA0111.10.878
MA0112.20.00173
MA0113.10.584
MA0114.10.0148
MA0115.10.6
MA0116.10.00129
MA0117.10.64
MA0119.10.539
MA0122.10.627
MA0124.10.991
MA0125.10.64
MA0131.10.684
MA0135.10.469
MA0136.14.39472e-8
MA0137.20.0976
MA0138.20.843
MA0139.10.552
MA0140.10.105
MA0141.10.00524
MA0142.10.437
MA0143.10.0196
MA0144.10.86
MA0145.10.416
MA0146.10.0765
MA0147.10.197
MA0148.10.86
MA0149.10.0147
MA0150.17.60868e-5
MA0152.10.41
MA0153.10.111
MA0154.10.0476
MA0155.10.514
MA0156.14.85463e-6
MA0157.10.146
MA0159.10.0279
MA0160.10.0351
MA0162.10.193
MA0163.13.34007e-8
MA0164.10.688
MA0258.10.0483
MA0259.10.773



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: CNhs12318

Novel motifP-value
10.164
100.101
1000.725
1010.385
1020.953
1030.0171
1040.0981
1050.0978
1060.0104
1070.149
1080.893
1090.00121
110.0139
1100.0653
1110.5
1120.257
1130.0688
1140.276
1150.892
1160.411
1170.0324
1180.413
1190.644
120.211
1200.166
1210.467
1220.737
1230.0219
1240.526
1250.849
1260.126
1270.3
1280.127
1290.427
130.0091
1300.112
1310.021
1320.261
1330.192
1340.383
1350.265
1360.00209
1370.84
1380.961
1390.442
140.928
1400.797
1410.447
1420.406
1430.0238
1440.53
1450.596
1460.567
1470.773
1480.859
1490.125
150.0656
1500.0729
1510.933
1520.0746
1530.905
1540.182
1550.921
1560.403
1570.31
1580.0858
1590.00307
160.0297
1600.224
1610.301
1620.703
1630.578
1640.0323
1650.197
1660.739
1670.485
1680.89
1690.0579
170.0701
180.0376
190.479
20.781
200.321
210.058
220.276
230.324
240.0435
250.587
260.0635
270.336
280.921
290.00251
30.143
300.499
310.975
320.00856
330.0759
340.692
350.539
360.424
370.054
380.682
390.314
40.863
400.166
410.296
420.416
430.175
440.0848
450.59
460.0302
470.134
480.133
490.695
50.788
500.687
510.308
520.626
530.168
540.752
550.892
560.729
570.619
580.431
590.0481
60.494
600.115
610.237
620.191
630.666
640.132
650.355
660.0634
670.498
680.337
690.471
70.142
700.19
710.0122
720.159
730.0422
740.623
750.0218
760.342
770.123
780.00393
790.54
80.0669
800.325
810.632
820.789
830.0853
840.471
850.848
860.197
872.19812e-4
880.562
890.0771
90.265
900.366
910.677
920.573
930.884
940.273
950.02
960.547
970.771
980.237
990.566



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: CNhs12318


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
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000125 (neural nucleus)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001890 (forebrain)
0001891 (midbrain)
0001893 (telencephalon)
0002020 (gray matter)
0002038 (substantia nigra)
0002050 (embryonic structure)
0002298 (brainstem)
0002308 (nucleus of brain)
0002346 (neurectoderm)
0002420 (basal ganglion)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0002950 (regional part of midbrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0003528 (brain grey matter)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006331 (brainstem nucleus)
0006598 (presumptive structure)
0007023 (adult organism)
0007135 (neural keel)
0007284 (presumptive neural plate)

FF: FANTOM5
NA

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
NA

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