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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120

Revision as of 16:31, 29 March 2012


Name:malignant trichilemmal cyst cell line:DJM-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuehair follicle
dev stage87 year old adult
sexfemale
age87
cell typehair follicle, outer root sheath cell
cell lineDJM-1
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
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs10730

Jaspar motifP-value
MA0002.20.495
MA0003.10.477
MA0004.10.323
MA0006.10.353
MA0007.10.0668
MA0009.10.394
MA0014.10.567
MA0017.10.408
MA0018.20.657
MA0019.10.139
MA0024.10.0222
MA0025.10.113
MA0027.10.525
MA0028.12.75103e-5
MA0029.10.56
MA0030.10.346
MA0031.10.0251
MA0035.20.891
MA0038.10.0818
MA0039.20.0305
MA0040.10.738
MA0041.10.636
MA0042.10.789
MA0043.10.649
MA0046.10.259
MA0047.20.24
MA0048.10.948
MA0050.12.49677e-10
MA0051.11.86609e-9
MA0052.10.911
MA0055.10.118
MA0057.10.405
MA0058.10.607
MA0059.10.284
MA0060.10.00345
MA0061.10.397
MA0062.21.62871e-4
MA0065.20.496
MA0066.10.151
MA0067.10.204
MA0068.10.835
MA0069.10.0765
MA0070.10.848
MA0071.10.302
MA0072.10.814
MA0073.10.947
MA0074.10.348
MA0076.11.69639e-5
MA0077.10.67
MA0078.10.7
MA0079.20.261
MA0080.20.291
MA0081.10.346
MA0083.10.367
MA0084.10.13
MA0087.10.693
MA0088.10.24
MA0090.10.00226
MA0091.10.00339
MA0092.10.817
MA0093.10.42
MA0099.22.08806e-13
MA0100.10.162
MA0101.10.346
MA0102.20.481
MA0103.14.14076e-6
MA0104.20.0736
MA0105.10.22
MA0106.10.00101
MA0107.10.264
MA0108.20.939
MA0111.10.227
MA0112.20.744
MA0113.10.0433
MA0114.10.766
MA0115.10.757
MA0116.10.16
MA0117.10.399
MA0119.10.0596
MA0122.10.315
MA0124.10.879
MA0125.10.477
MA0131.10.851
MA0135.10.446
MA0136.10.206
MA0137.20.192
MA0138.20.0785
MA0139.10.107
MA0140.10.278
MA0141.10.0684
MA0142.10.0345
MA0143.10.995
MA0144.10.609
MA0145.10.0329
MA0146.10.649
MA0147.10.0443
MA0148.10.0454
MA0149.10.0366
MA0150.10.146
MA0152.10.321
MA0153.10.478
MA0154.10.865
MA0155.10.166
MA0156.10.0039
MA0157.10.054
MA0159.10.109
MA0160.10.988
MA0162.10.942
MA0163.10.532
MA0164.10.498
MA0258.10.159
MA0259.10.564



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: CNhs10730

Novel motifP-value
10.608
100.553
1000.417
1010.428
1020.362
1030.92
1040.341
1050.3
1060.305
1070.253
1080.881
1090.266
110.179
1100.688
1110.403
1120.301
1130.297
1140.206
1150.708
1160.102
1170.923
1180.434
1190.786
120.355
1200.855
1210.836
1220.328
1230.0621
1240.858
1250.382
1260.847
1270.62
1280.842
1290.225
130.00269
1300.256
1310.64
1320.998
1330.0219
1340.127
1350.717
1360.958
1370.233
1380.63
1390.101
140.97
1400.629
1410.426
1420.928
1430.19
1440.0771
1450.588
1460.277
1470.682
1480.899
1490.25
150.845
1500.203
1510.235
1520.616
1530.977
1540.88
1550.789
1560.652
1570.855
1580.65
1590.317
160.999
1600.605
1610.25
1620.111
1630.465
1640.498
1650.835
1660.727
1670.354
1680.729
1690.674
170.342
180.454
190.0863
20.702
200.879
210.645
220.56
230.201
240.134
250.625
260.198
270.925
280.222
290.104
30.827
300.351
310.221
320.00144
330.213
340.185
350.413
360.0962
370.715
380.42
390.856
40.801
400.336
410.226
420.27
430.904
440.0791
450.13
460.994
470.863
480.828
490.828
50.776
500.274
510.308
520.207
530.407
540.221
550.328
560.307
570.111
580.465
590.122
60.84
600.227
610.701
620.9
630.319
640.841
650.775
660.00216
670.465
680.0284
690.468
70.205
700.108
710.545
720.814
730.945
740.239
750.00716
760.776
770.283
780.0178
791.99766e-4
80.162
800.887
810.153
820.118
830.709
840.972
850.209
860.574
870.336
880.756
890.579
90.381
900.779
910.0358
920.992
930.998
940.741
950.879
960.305
970.277
980.713
990.998



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: CNhs10730


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)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
1749 (squamous cell carcinoma)
305 (carcinoma)
4 (disease)

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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