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FF:10154-103A1: 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 17:14, 29 March 2012


Name:thalamus, 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
tissuethalamus
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-Neural0.181
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-penis0.957
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-0.306
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0427
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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: CNhs12314

Jaspar motifP-value
MA0002.20.0437
MA0003.10.192
MA0004.10.323
MA0006.10.306
MA0007.10.518
MA0009.10.115
MA0014.10.704
MA0017.10.00114
MA0018.20.58
MA0019.10.921
MA0024.10.611
MA0025.10.962
MA0027.10.533
MA0028.10.0587
MA0029.10.0297
MA0030.10.108
MA0031.10.147
MA0035.20.00781
MA0038.10.272
MA0039.20.166
MA0040.10.844
MA0041.10.431
MA0042.10.923
MA0043.10.856
MA0046.10.00141
MA0047.20.468
MA0048.10.134
MA0050.10.145
MA0051.10.232
MA0052.10.542
MA0055.16.49112e-4
MA0057.10.804
MA0058.10.387
MA0059.10.0704
MA0060.10.356
MA0061.10.00352
MA0062.20.0029
MA0065.26.72148e-4
MA0066.10.00677
MA0067.10.886
MA0068.10.748
MA0069.10.77
MA0070.10.593
MA0071.10.0136
MA0072.10.349
MA0073.10.522
MA0074.10.243
MA0076.10.116
MA0077.10.00762
MA0078.10.805
MA0079.20.894
MA0080.21.05347e-6
MA0081.10.0249
MA0083.10.00698
MA0084.10.176
MA0087.10.287
MA0088.10.355
MA0090.10.193
MA0091.10.548
MA0092.10.214
MA0093.10.375
MA0099.21.36423e-24
MA0100.10.528
MA0101.10.00229
MA0102.20.103
MA0103.10.052
MA0104.20.406
MA0105.13.1952e-4
MA0106.10.0216
MA0107.10.00169
MA0108.20.0579
MA0111.10.782
MA0112.20.00106
MA0113.10.964
MA0114.10.00278
MA0115.10.746
MA0116.10.00375
MA0117.10.761
MA0119.10.254
MA0122.10.78
MA0124.10.93
MA0125.10.444
MA0131.10.937
MA0135.10.325
MA0136.11.48527e-10
MA0137.20.246
MA0138.20.549
MA0139.10.494
MA0140.10.00787
MA0141.10.0019
MA0142.10.429
MA0143.10.0387
MA0144.10.692
MA0145.10.276
MA0146.10.0319
MA0147.10.225
MA0148.10.422
MA0149.10.0137
MA0150.14.35556e-5
MA0152.10.571
MA0153.10.236
MA0154.10.0495
MA0155.10.57
MA0156.13.82932e-7
MA0157.10.68
MA0159.10.0115
MA0160.10.012
MA0162.10.131
MA0163.19.4947e-7
MA0164.10.679
MA0258.10.018
MA0259.10.724



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: CNhs12314

Novel motifP-value
10.074
100.0567
1000.371
1010.401
1020.925
1030.0505
1040.104
1050.158
1060.0249
1070.129
1080.918
1099.81437e-4
110.00877
1100.0519
1110.219
1120.332
1130.332
1140.191
1150.823
1160.144
1170.0157
1180.27
1190.297
120.49
1200.206
1210.392
1220.828
1230.274
1240.266
1250.542
1260.046
1270.4
1280.169
1290.51
130.00362
1300.34
1310.0417
1320.425
1330.115
1340.472
1350.184
1368.82695e-4
1370.887
1380.915
1390.281
140.923
1400.982
1410.415
1420.353
1430.0409
1440.697
1450.29
1460.624
1470.804
1480.475
1490.28
150.0687
1500.108
1510.822
1520.0656
1530.89
1540.278
1550.958
1560.412
1570.409
1580.0857
1590.00477
160.0268
1600.237
1610.364
1620.654
1630.916
1640.0136
1650.168
1660.812
1670.903
1680.741
1690.0227
170.0905
180.0546
190.264
20.903
200.144
210.0383
220.227
230.389
240.0453
250.544
260.00313
270.517
280.855
290.00332
30.0684
300.925
310.91
320.00961
330.0461
340.675
350.614
360.241
370.0312
380.441
390.3
40.793
400.0541
410.312
420.265
430.141
440.123
450.68
460.0513
470.0791
480.063
490.384
50.928
500.481
510.387
520.592
530.474
540.536
550.727
560.596
570.405
580.362
590.0554
60.797
600.0864
610.137
620.207
630.338
640.138
650.266
660.112
670.329
680.446
690.262
70.121
700.0628
710.00918
720.272
730.0249
740.869
750.0263
760.332
770.118
780.00189
790.361
80.0604
800.437
810.509
820.636
830.0468
840.572
850.366
860.211
871.07957e-4
880.628
890.165
90.366
900.0702
910.737
920.448
930.904
940.209
950.0116
960.774
970.744
980.222
990.588



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: CNhs12314


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)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
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)
0001894 (diencephalon)
0001897 (dorsal plus ventral thalamus)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
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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