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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001003,UBERON:0001062,UBERON:0002050,UBERON:0002097,UBERON:0002199,UBERON:0002416,UBERON:0002532,UBERON:0003102,UBERON:0004121,UBERON:0005423,UBERON:0007376,UBERON:0007383
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001003,UBERON:0001062,UBERON:0002050,UBERON:0002097,UBERON:0002199,UBERON:0002416,UBERON:0002532,UBERON:0003102,UBERON:0004121,UBERON:0005423,UBERON:0007376,UBERON:0007383
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100849
|fonse_cell_line=FF:0100849
|fonse_cell_line_closure=FF:0100849
|fonse_cell_line_closure=FF:0100849

Revision as of 16:43, 29 March 2012


Name:melanoma cell line:COLO 679
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stageNA
sexfemale
age47
cell typemelanocyte
cell lineCOLO 679
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-penis0.0294
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: CNhs11281

Jaspar motifP-value
MA0002.20.229
MA0003.10.472
MA0004.12.36134e-4
MA0006.10.155
MA0007.10.732
MA0009.10.38
MA0014.10.812
MA0017.10.029
MA0018.20.0466
MA0019.10.847
MA0024.10.0532
MA0025.10.0962
MA0027.10.933
MA0028.11.6053e-7
MA0029.10.711
MA0030.10.406
MA0031.10.69
MA0035.20.0151
MA0038.10.0061
MA0039.20.996
MA0040.10.172
MA0041.10.0565
MA0042.10.232
MA0043.10.12
MA0046.10.0305
MA0047.20.673
MA0048.10.129
MA0050.10.194
MA0051.10.827
MA0052.10.00111
MA0055.10.141
MA0057.10.667
MA0058.12.06296e-9
MA0059.12.40665e-5
MA0060.15.22804e-4
MA0061.10.00358
MA0062.21.82767e-11
MA0065.20.27
MA0066.10.743
MA0067.10.00749
MA0068.10.0164
MA0069.10.556
MA0070.10.109
MA0071.10.622
MA0072.10.691
MA0073.10.568
MA0074.10.806
MA0076.13.25505e-9
MA0077.10.458
MA0078.10.243
MA0079.20.244
MA0080.20.00101
MA0081.10.496
MA0083.10.0984
MA0084.10.426
MA0087.10.878
MA0088.10.02
MA0090.10.442
MA0091.10.0185
MA0092.10.034
MA0093.11.85723e-5
MA0099.23.0302e-4
MA0100.10.0755
MA0101.10.105
MA0102.20.0423
MA0103.10.00571
MA0104.24.50426e-5
MA0105.10.0138
MA0106.10.592
MA0107.10.0214
MA0108.20.692
MA0111.10.697
MA0112.20.00832
MA0113.10.162
MA0114.10.431
MA0115.10.466
MA0116.10.00525
MA0117.10.527
MA0119.10.582
MA0122.10.569
MA0124.10.958
MA0125.10.16
MA0131.10.132
MA0135.10.129
MA0136.10.399
MA0137.20.641
MA0138.20.052
MA0139.10.271
MA0140.10.0997
MA0141.10.3
MA0142.10.949
MA0143.10.555
MA0144.10.516
MA0145.10.0524
MA0146.10.529
MA0147.15.77329e-5
MA0148.10.538
MA0149.10.328
MA0150.10.0378
MA0152.10.231
MA0153.10.0927
MA0154.10.0102
MA0155.10.0523
MA0156.10.0715
MA0157.10.84
MA0159.10.419
MA0160.10.772
MA0162.10.0115
MA0163.10.215
MA0164.10.919
MA0258.10.0878
MA0259.10.00806



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: CNhs11281

Novel motifP-value
10.973
100.818
1000.679
1010.821
1020.136
1030.731
1040.981
1050.0717
1060.0213
1070.0921
1080.669
1090.93
110.39
1100.741
1110.0425
1120.58
1130.058
1140.0225
1150.573
1160.218
1170.289
1180.636
1190.075
120.149
1200.196
1210.62
1220.323
1230.231
1240.571
1250.259
1260.442
1270.224
1280.0199
1290.539
130.639
1300.591
1310.142
1320.412
1330.123
1340.763
1350.533
1360.0127
1370.325
1380.43
1390.0223
140.515
1400.0912
1410.854
1420.653
1430.0614
1440.614
1450.655
1460.5
1470.821
1480.879
1490.453
150.239
1500.311
1510.39
1520.611
1530.592
1540.596
1550.349
1560.524
1570.777
1580.704
1590.0896
160.94
1600.0458
1610.0378
1620.648
1630.661
1640.728
1650.25
1660.0613
1670.912
1680.445
1690.206
170.136
180.57
190.0843
20.155
200.112
210.297
220.519
230.0721
240.545
250.764
260.936
270.193
280.649
290.683
30.478
300.21
310.51
321.38527e-4
330.976
340.219
350.957
360.558
370.939
380.569
390.38
40.688
400.0664
410.926
420.537
430.127
440.305
450.219
460.297
470.738
480.604
490.256
50.824
500.714
510.125
520.116
530.369
540.38
550.719
560.701
570.932
580.226
590.279
60.0487
600.167
610.709
620.0972
630.152
640.531
650.213
660.0641
670.576
680.00331
690.329
70.668
700.438
710.524
720.32
730.784
740.446
750.25
760.499
770.0293
780.246
790.0436
80.234
800.689
810.163
820.0256
830.0679
840.776
850.508
860.513
870.0756
880.408
890.122
90.281
900.806
910.0452
920.108
930.745
940.066
950.295
960.263
970.743
980.221
990.581



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: CNhs11281


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

DOID: Disease
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001003 (skin epidermis)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002097 (skin of body)
0002199 (integument)
0002416 (integumental system)
0002532 (epiblast (generic))
0003102 (surface structure)
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)
0007376 (outer epithelium)
0007383 (enveloping layer of ectoderm)

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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