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FF:10161-103A8: 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:globus pallidus, 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
tissueglobus pallidus
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-Neural0.149
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-penis1.014
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.277
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs12319

Jaspar motifP-value
MA0002.20.0482
MA0003.10.193
MA0004.10.372
MA0006.10.354
MA0007.10.704
MA0009.10.108
MA0014.10.757
MA0017.10.00173
MA0018.20.674
MA0019.10.571
MA0024.10.459
MA0025.10.546
MA0027.10.664
MA0028.10.102
MA0029.10.092
MA0030.10.172
MA0031.10.111
MA0035.20.0165
MA0038.10.309
MA0039.20.237
MA0040.10.946
MA0041.10.423
MA0042.10.894
MA0043.10.798
MA0046.10.00414
MA0047.20.537
MA0048.10.174
MA0050.10.273
MA0051.10.238
MA0052.10.343
MA0055.10.00241
MA0057.10.827
MA0058.10.475
MA0059.10.099
MA0060.10.233
MA0061.10.00246
MA0062.20.009
MA0065.27.65371e-4
MA0066.10.00641
MA0067.10.884
MA0068.10.71
MA0069.10.817
MA0070.10.578
MA0071.10.0177
MA0072.10.307
MA0073.10.55
MA0074.10.253
MA0076.10.194
MA0077.10.00384
MA0078.10.692
MA0079.20.848
MA0080.22.82719e-5
MA0081.10.0347
MA0083.10.00795
MA0084.10.183
MA0087.10.479
MA0088.10.444
MA0090.10.233
MA0091.10.598
MA0092.10.225
MA0093.10.452
MA0099.26.86362e-22
MA0100.10.52
MA0101.10.00249
MA0102.20.223
MA0103.10.0356
MA0104.20.444
MA0105.11.17671e-4
MA0106.10.0273
MA0107.10.00138
MA0108.20.0514
MA0111.10.769
MA0112.29.48882e-4
MA0113.10.92
MA0114.10.00403
MA0115.10.793
MA0116.10.00237
MA0117.10.698
MA0119.10.282
MA0122.10.701
MA0124.10.97
MA0125.10.528
MA0131.10.879
MA0135.10.134
MA0136.11.11132e-8
MA0137.20.0168
MA0138.20.768
MA0139.10.376
MA0140.10.0308
MA0141.10.00411
MA0142.10.583
MA0143.10.0611
MA0144.10.831
MA0145.10.267
MA0146.10.0432
MA0147.10.244
MA0148.10.432
MA0149.10.0143
MA0150.14.45801e-5
MA0152.10.469
MA0153.10.245
MA0154.10.0404
MA0155.10.556
MA0156.11.81775e-5
MA0157.10.547
MA0159.10.0102
MA0160.10.0242
MA0162.10.135
MA0163.13.4145e-7
MA0164.10.737
MA0258.10.0237
MA0259.10.75



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: CNhs12319

Novel motifP-value
10.0834
100.0661
1000.53
1010.438
1020.998
1030.0196
1040.118
1050.148
1060.0188
1070.13
1080.977
1090.00143
110.0113
1100.0544
1110.295
1120.265
1130.309
1140.171
1150.852
1160.234
1170.0164
1180.281
1190.391
120.521
1200.188
1210.433
1220.911
1230.16
1240.522
1250.64
1260.0627
1270.396
1280.171
1290.485
130.00519
1300.252
1310.0159
1320.383
1330.1
1340.643
1350.395
1360.00197
1370.874
1380.806
1390.39
140.931
1400.61
1410.461
1420.389
1430.0395
1440.646
1450.423
1460.69
1470.837
1480.48
1490.149
150.0708
1500.104
1510.825
1520.0726
1530.805
1540.264
1550.985
1560.434
1570.428
1580.117
1590.00517
160.0216
1600.209
1610.355
1620.69
1630.717
1640.0207
1650.176
1660.991
1670.805
1680.675
1690.0234
170.0924
180.0417
190.281
20.857
200.226
210.0646
220.225
230.347
240.0276
250.543
260.00706
270.363
280.882
290.00291
30.0687
300.755
310.893
320.00859
330.0587
340.677
350.54
360.321
370.0339
380.552
390.311
40.979
400.094
410.242
420.292
430.131
440.0593
450.642
460.04
470.113
480.0904
490.403
50.915
500.544
510.34
520.557
530.349
540.558
550.758
560.619
570.397
580.302
590.0455
60.615
600.0816
610.161
620.16
630.386
640.11
650.293
660.113
670.327
680.274
690.288
70.111
700.0674
710.00919
720.213
730.0289
740.879
750.0235
760.37
770.113
780.00344
790.3
80.0539
800.306
810.486
820.623
830.0505
840.579
850.409
860.198
871.33267e-4
880.627
890.121
90.314
900.08
910.86
920.375
930.765
940.155
950.0128
960.707
970.743
980.253
990.523



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: CNhs12319


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)
0001869 (cerebral hemisphere)
0001875 (globus pallidus)
0001890 (forebrain)
0001893 (telencephalon)
0002020 (gray matter)
0002050 (embryonic structure)
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)
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)
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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