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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:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,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 16:55, 29 March 2012


Name:glassy cell carcinoma cell line:HOKUG
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecervix
dev stageNA
sexfemale
age53
cell typeunclassifiable
cell lineHOKUG
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-penis0.64
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-lymphoma0.263
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: CNhs11824

Jaspar motifP-value
MA0002.20.00249
MA0003.10.944
MA0004.10.0753
MA0006.10.0629
MA0007.10.403
MA0009.10.337
MA0014.10.0831
MA0017.10.795
MA0018.20.547
MA0019.10.847
MA0024.11.63434e-5
MA0025.10.396
MA0027.10.832
MA0028.10.00498
MA0029.10.55
MA0030.10.149
MA0031.10.736
MA0035.20.74
MA0038.10.182
MA0039.20.0131
MA0040.10.0815
MA0041.10.724
MA0042.10.682
MA0043.10.412
MA0046.10.781
MA0047.20.881
MA0048.10.828
MA0050.10.253
MA0051.10.94
MA0052.10.0995
MA0055.10.00368
MA0057.10.166
MA0058.10.0214
MA0059.10.0158
MA0060.10.198
MA0061.15.78282e-6
MA0062.20.0331
MA0065.20.288
MA0066.10.36
MA0067.10.304
MA0068.10.0438
MA0069.10.787
MA0070.10.466
MA0071.10.655
MA0072.10.233
MA0073.10.405
MA0074.10.703
MA0076.10.00314
MA0077.10.538
MA0078.10.143
MA0079.20.317
MA0080.28.81462e-8
MA0081.10.0291
MA0083.10.85
MA0084.10.0254
MA0087.10.744
MA0088.10.198
MA0090.10.0302
MA0091.10.0228
MA0092.10.308
MA0093.10.102
MA0099.20.747
MA0100.10.838
MA0101.10.00283
MA0102.20.0478
MA0103.14.34335e-7
MA0104.20.0419
MA0105.12.84861e-8
MA0106.10.00544
MA0107.12.93981e-4
MA0108.20.443
MA0111.10.791
MA0112.20.704
MA0113.10.799
MA0114.10.155
MA0115.10.211
MA0116.12.17548e-4
MA0117.10.217
MA0119.10.596
MA0122.10.769
MA0124.10.598
MA0125.10.185
MA0131.10.991
MA0135.10.197
MA0136.18.49065e-5
MA0137.20.399
MA0138.20.323
MA0139.10.74
MA0140.10.0782
MA0141.10.816
MA0142.10.0762
MA0143.10.683
MA0144.10.665
MA0145.10.0903
MA0146.10.18
MA0147.10.043
MA0148.10.395
MA0149.10.0684
MA0150.10.956
MA0152.10.0929
MA0153.10.723
MA0154.17.76271e-4
MA0155.10.446
MA0156.10.123
MA0157.10.202
MA0159.10.439
MA0160.10.709
MA0162.10.781
MA0163.16.20478e-4
MA0164.10.33
MA0258.10.72
MA0259.10.285



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: CNhs11824

Novel motifP-value
10.95
100.883
1000.748
1010.4
1020.128
1030.298
1040.394
1050.891
1060.219
1070.574
1080.789
1090.0695
110.0798
1100.964
1110.953
1120.267
1130.134
1140.136
1150.979
1160.866
1170.943
1180.469
1190.201
120.632
1200.994
1210.264
1220.183
1230.618
1240.038
1250.183
1260.906
1270.495
1280.0915
1290.496
130.0457
1300.88
1310.647
1320.603
1330.00308
1340.758
1350.0847
1360.00669
1370.146
1380.429
1390.295
140.876
1400.687
1410.348
1420.464
1430.00184
1440.356
1450.218
1460.718
1470.897
1480.118
1490.171
150.314
1500.733
1510.405
1520.302
1530.314
1540.737
1550.442
1560.488
1570.395
1580.259
1590.746
160.704
1600.501
1610.694
1620.695
1630.778
1640.599
1650.858
1660.378
1670.977
1680.11
1690.469
170.907
180.23
190.0803
20.992
200.201
210.703
220.945
230.103
240.975
250.656
260.564
270.408
280.622
290.816
30.256
300.32
310.156
320.017
330.844
340.418
350.0459
360.46
370.328
380.855
390.915
40.648
400.427
410.003
420.488
430.0805
440.496
450.956
460.236
470.379
480.662
490.0867
50.338
500.646
510.341
520.39
530.184
540.794
550.668
560.919
570.88
580.972
590.182
60.555
600.931
610.929
620.36
630.743
640.604
650.239
660.848
670.483
680.209
690.389
70.262
700.795
710.766
720.94
730.406
740.00173
750.661
760.429
770.508
780.089
790.0914
80.842
800.0822
810.0867
820.0205
830.16
840.995
850.0133
860.335
870.109
880.26
890.64
90.319
900.092
910.0779
920.216
930.571
940.0719
950.299
960.0489
970.59
980.197
990.861



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: CNhs11824


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)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
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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