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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
Line 8: Line 7:
|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 16:50, 29 March 2012


Name:clear cell carcinoma cell line:JHOC-5
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueovary
dev stageNA
sexfemale
age54
cell typeunclassifiable
cell lineJHOC-5
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-penis0.18
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-lymphoma0.436
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs11745

Jaspar motifP-value
MA0002.20.154
MA0003.10.252
MA0004.10.64
MA0006.10.957
MA0007.10.465
MA0009.10.847
MA0014.10.0984
MA0017.10.502
MA0018.20.00341
MA0019.10.326
MA0024.18.26515e-4
MA0025.10.582
MA0027.10.929
MA0028.10.0501
MA0029.10.84
MA0030.10.0468
MA0031.10.0436
MA0035.20.661
MA0038.10.687
MA0039.20.444
MA0040.10.0879
MA0041.10.0871
MA0042.10.101
MA0043.10.101
MA0046.12.11548e-7
MA0047.20.19
MA0048.10.0753
MA0050.10.295
MA0051.10.677
MA0052.11.82554e-4
MA0055.19.56737e-4
MA0057.10.484
MA0058.10.455
MA0059.10.286
MA0060.10.271
MA0061.10.00281
MA0062.20.759
MA0065.20.0605
MA0066.10.43
MA0067.10.11
MA0068.10.00748
MA0069.10.644
MA0070.10.85
MA0071.10.187
MA0072.10.88
MA0073.10.784
MA0074.10.458
MA0076.10.321
MA0077.10.298
MA0078.10.299
MA0079.20.243
MA0080.22.40051e-7
MA0081.10.0386
MA0083.13.40321e-4
MA0084.10.572
MA0087.10.337
MA0088.10.0147
MA0090.10.253
MA0091.10.137
MA0092.10.271
MA0093.10.613
MA0099.20.843
MA0100.10.198
MA0101.10.00949
MA0102.20.0887
MA0103.14.81465e-6
MA0104.20.209
MA0105.12.47323e-4
MA0106.10.0356
MA0107.10.0268
MA0108.24.85898e-9
MA0111.10.333
MA0112.20.251
MA0113.10.15
MA0114.10.191
MA0115.10.408
MA0116.10.00857
MA0117.10.315
MA0119.10.653
MA0122.10.728
MA0124.10.171
MA0125.10.583
MA0131.10.532
MA0135.10.0739
MA0136.11.54968e-6
MA0137.20.226
MA0138.20.0385
MA0139.10.00149
MA0140.10.289
MA0141.10.195
MA0142.10.716
MA0143.10.322
MA0144.10.395
MA0145.10.738
MA0146.10.605
MA0147.10.104
MA0148.10.944
MA0149.10.011
MA0150.10.966
MA0152.10.626
MA0153.15.40342e-12
MA0154.10.343
MA0155.10.801
MA0156.17.77035e-4
MA0157.10.0202
MA0159.10.0925
MA0160.10.603
MA0162.10.182
MA0163.10.0651
MA0164.10.878
MA0258.10.382
MA0259.10.325



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: CNhs11745

Novel motifP-value
10.0898
100.111
1000.00105
1010.178
1020.638
1030.411
1040.962
1050.143
1060.701
1070.276
1080.534
1090.0551
110.163
1100.0531
1110.15
1120.5
1130.0218
1140.84
1150.336
1160.39
1170.154
1180.0148
1190.159
120.324
1200.0979
1210.54
1220.263
1230.557
1240.286
1250.272
1260.4
1270.77
1280.766
1290.272
138.78508e-4
1300.806
1310.931
1320.852
1330.113
1340.104
1350.0204
1360.0104
1370.349
1380.777
1390.0936
140.728
1400.788
1410.675
1420.807
1430.0422
1440.925
1450.5
1460.236
1470.94
1480.569
1490.711
150.306
1500.603
1510.8
1520.327
1530.775
1540.404
1550.924
1560.971
1570.426
1580.178
1590.188
160.308
1600.159
1610.58
1620.69
1630.876
1640.0142
1650.826
1660.996
1670.189
1680.8
1690.8
170.931
180.959
190.914
20.205
200.0313
210.108
220.307
230.878
240.446
250.983
260.0271
270.352
280.711
290.0269
30.503
300.882
310.46
320.337
330.0474
340.0928
350.907
360.123
370.12
380.696
390.509
40.996
400.0222
410.027
420.548
430.964
440.023
450.34
460.419
470.145
480.0763
490.424
50.731
500.628
510.868
520.437
530.315
540.741
550.697
560.757
570.354
580.683
590.722
60.339
600.674
610.627
620.732
630.461
640.526
650.975
660.515
670.906
680.98
690.518
70.63
700.275
710.169
720.264
730.863
740.559
750.0979
760.174
770.317
780.119
790.843
80.457
800.00174
810.714
820.445
830.904
840.902
850.372
860.587
870.0898
880.498
890.923
90.0955
900.208
910.177
920.993
930.38
940.286
950.229
960.769
970.787
980.511
990.362



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: CNhs11745


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
0050686 (organ system cancer)
0050687 (cell type cancer)
120 (female reproductive organ cancer)
14566 (disease of cellular proliferation)
162 (cancer)
193 (reproductive organ cancer)
299 (adenocarcinoma)
305 (carcinoma)
4 (disease)
4468 (clear cell adenocarcinoma)

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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