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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101522
|fonse_cell_line=FF:0101522
|fonse_cell_line_closure=FF:0101522
|fonse_cell_line_closure=FF:0101522

Revision as of 16:54, 29 March 2012


Name:xeroderma pigentosum b cell line:XPL 17
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexunknown
ageNA
cell typeb cell
cell lineXPL 17
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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-penis0.327
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-lymphoma0.225
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11813

Jaspar motifP-value
MA0002.25.9492e-4
MA0003.10.578
MA0004.10.122
MA0006.10.634
MA0007.10.492
MA0009.10.603
MA0014.10.999
MA0017.10.0859
MA0018.20.0175
MA0019.10.361
MA0024.10.235
MA0025.10.061
MA0027.10.496
MA0028.10.00727
MA0029.10.551
MA0030.10.0377
MA0031.10.0299
MA0035.20.859
MA0038.10.918
MA0039.20.89
MA0040.10.199
MA0041.10.141
MA0042.10.373
MA0043.10.00452
MA0046.10.167
MA0047.20.307
MA0048.10.851
MA0050.11.53921e-21
MA0051.16.1582e-16
MA0052.10.75
MA0055.10.115
MA0057.10.987
MA0058.10.118
MA0059.10.00987
MA0060.10.07
MA0061.15.62198e-9
MA0062.21.24885e-6
MA0065.20.0109
MA0066.10.242
MA0067.10.672
MA0068.10.0878
MA0069.10.423
MA0070.10.302
MA0071.10.695
MA0072.10.844
MA0073.10.451
MA0074.10.716
MA0076.10.00329
MA0077.10.336
MA0078.10.25
MA0079.20.426
MA0080.28.88022e-8
MA0081.10.0387
MA0083.10.324
MA0084.10.291
MA0087.10.162
MA0088.10.0309
MA0090.12.78236e-5
MA0091.10.962
MA0092.10.921
MA0093.10.154
MA0099.20.0651
MA0100.10.684
MA0101.15.18614e-10
MA0102.20.116
MA0103.10.00793
MA0104.20.0233
MA0105.17.74521e-12
MA0106.10.0225
MA0107.12.64165e-11
MA0108.26.19976e-6
MA0111.10.433
MA0112.20.0215
MA0113.10.973
MA0114.10.0353
MA0115.10.717
MA0116.19.85995e-5
MA0117.10.645
MA0119.10.504
MA0122.10.815
MA0124.10.424
MA0125.10.487
MA0131.10.655
MA0135.10.277
MA0136.14.44063e-9
MA0137.20.744
MA0138.20.488
MA0139.10.222
MA0140.10.805
MA0141.10.064
MA0142.10.186
MA0143.10.755
MA0144.10.671
MA0145.10.841
MA0146.10.174
MA0147.10.0118
MA0148.10.141
MA0149.10.271
MA0150.10.56
MA0152.10.111
MA0153.10.00143
MA0154.11.82544e-4
MA0155.10.919
MA0156.12.45376e-6
MA0157.10.0555
MA0159.10.0845
MA0160.10.0717
MA0162.10.412
MA0163.18.57005e-14
MA0164.10.958
MA0258.10.0209
MA0259.10.18



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: CNhs11813

Novel motifP-value
10.0172
100.0348
1000.547
1010.21
1020.45
1030.276
1040.968
1050.945
1060.152
1070.435
1080.742
1090.0159
110.0583
1100.121
1110.00596
1120.0722
1130.465
1140.131
1150.431
1160.321
1170.0209
1180.0771
1190.0387
120.892
1200.446
1210.47
1220.284
1230.00382
1240.226
1250.0268
1260.119
1270.182
1280.437
1290.415
130.209
1300.913
1310.995
1320.957
1330.627
1340.932
1350.901
1360.553
1370.284
1380.555
1390.0624
140.587
1400.197
1410.192
1420.845
1430.0502
1440.873
1450.335
1460.586
1470.247
1480.105
1490.743
150.0858
1500.754
1510.876
1520.986
1530.789
1540.762
1550.105
1560.695
1570.527
1580.395
1590.338
160.537
1600.117
1610.0175
1620.967
1630.649
1640.16
1650.851
1660.453
1670.305
1680.586
1690.0887
170.391
180.338
190.782
20.945
200.554
210.13
220.702
230.927
240.165
250.208
260.0611
270.443
280.502
290.0147
30.0557
300.461
310.67
320.868
330.364
340.837
350.0915
360.0164
370.165
380.124
390.727
40.457
400.141
410.635
420.0638
430.199
440.0132
450.689
460.116
470.0232
480.0701
490.133
50.779
500.833
510.603
520.993
530.341
540.909
550.733
560.6
570.209
580.0702
590.13
60.748
600.386
610.0728
620.0776
630.322
640.146
650.253
660.704
670.353
680.258
690.924
70.195
700.172
710.0372
720.228
730.429
740.852
750.0229
760.438
770.576
780.186
790.87
80.139
800.541
810.241
820.352
830.927
840.174
850.664
860.215
870.112
880.625
890.414
90.968
900.0479
910.784
920.289
930.907
940.177
950.0364
960.433
970.223
980.168
990.703



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: CNhs11813


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000826 (pro-B cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000945 (lymphocyte of B lineage)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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