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FF:10173-103C2: 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 17:39, 29 March 2012


Name:cerebellum - 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
tissuecerebellum
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
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-penis0.284
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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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 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: CNhs13799

Jaspar motifP-value
MA0002.20.0573
MA0003.10.233
MA0004.10.21
MA0006.10.153
MA0007.10.263
MA0009.10.384
MA0014.10.639
MA0017.10.0122
MA0018.20.0412
MA0019.10.961
MA0024.10.413
MA0025.10.104
MA0027.10.982
MA0028.10.11
MA0029.10.212
MA0030.10.349
MA0031.10.476
MA0035.20.0735
MA0038.10.112
MA0039.20.15
MA0040.10.97
MA0041.10.167
MA0042.10.42
MA0043.10.623
MA0046.10.129
MA0047.20.111
MA0048.10.241
MA0050.11.22879e-4
MA0051.10.00257
MA0052.10.186
MA0055.10.0396
MA0057.10.453
MA0058.10.227
MA0059.10.063
MA0060.10.0303
MA0061.10.0121
MA0062.20.00263
MA0065.20.00239
MA0066.10.129
MA0067.10.701
MA0068.10.636
MA0069.10.916
MA0070.10.411
MA0071.10.255
MA0072.10.427
MA0073.10.243
MA0074.10.287
MA0076.10.172
MA0077.10.662
MA0078.10.764
MA0079.20.693
MA0080.21.50382e-9
MA0081.10.0617
MA0083.10.00119
MA0084.10.852
MA0087.10.85
MA0088.10.496
MA0090.10.0365
MA0091.10.624
MA0092.10.448
MA0093.10.233
MA0099.21.60268e-16
MA0100.10.738
MA0101.10.00407
MA0102.20.0373
MA0103.10.564
MA0104.20.739
MA0105.10.0116
MA0106.10.0266
MA0107.10.00402
MA0108.20.108
MA0111.10.724
MA0112.20.0037
MA0113.10.477
MA0114.10.00682
MA0115.10.689
MA0116.10.0188
MA0117.10.895
MA0119.10.157
MA0122.10.409
MA0124.10.757
MA0125.10.205
MA0131.10.895
MA0135.10.0785
MA0136.12.85012e-13
MA0137.20.511
MA0138.20.108
MA0139.10.795
MA0140.10.0449
MA0141.10.0214
MA0142.10.138
MA0143.10.129
MA0144.10.375
MA0145.10.141
MA0146.10.0247
MA0147.10.535
MA0148.10.138
MA0149.10.0681
MA0150.14.57065e-4
MA0152.10.494
MA0153.10.364
MA0154.10.0746
MA0155.10.306
MA0156.11.33623e-8
MA0157.10.92
MA0159.10.00534
MA0160.10.106
MA0162.10.101
MA0163.12.80036e-4
MA0164.10.809
MA0258.10.0442
MA0259.10.967



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: CNhs13799

Novel motifP-value
10.0791
100.073
1000.404
1010.677
1020.551
1030.0538
1040.0625
1050.121
1060.00472
1070.0227
1080.978
1099.90449e-4
110.0195
1100.0845
1110.372
1120.698
1130.316
1140.271
1150.759
1160.139
1170.00916
1180.248
1190.481
120.748
1200.176
1210.343
1220.674
1230.627
1240.2
1250.559
1260.047
1270.586
1280.165
1290.597
137.009e-4
1300.13
1310.0946
1320.91
1330.0238
1340.516
1350.415
1367.97203e-4
1370.348
1380.83
1390.266
140.615
1400.676
1410.837
1420.394
1430.0731
1440.875
1450.096
1460.391
1470.885
1480.0306
1490.123
150.0718
1500.171
1510.668
1520.0135
1530.99
1540.706
1550.426
1560.927
1570.343
1580.0714
1590.0328
160.0794
1600.201
1610.282
1620.819
1630.982
1640.0218
1650.0326
1660.645
1670.963
1680.516
1690.0228
170.0764
180.253
190.29
20.783
200.156
210.024
220.173
230.195
240.0418
250.54
264.09607e-5
270.841
280.869
290.0296
30.0502
300.964
310.962
320.0251
330.0594
340.598
350.88
360.325
370.0242
380.368
390.118
40.933
400.0598
410.452
420.359
430.128
440.178
450.722
460.0571
470.0805
480.0463
490.274
50.795
500.164
510.496
520.242
530.913
540.364
550.606
560.329
570.39
580.459
590.0494
60.816
600.0172
610.0646
620.231
630.083
640.401
650.294
660.252
670.324
680.326
690.337
70.0505
700.013
710.0128
720.259
730.00901
740.868
750.0526
760.418
770.0582
780.0218
790.346
80.0242
800.202
810.535
820.805
830.119
840.544
850.122
860.24
872.38143e-4
880.847
890.274
90.398
900.298
910.98
920.702
930.398
940.414
950.00769
960.898
970.686
980.721
990.228



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: CNhs13799


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

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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