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FF:11663-122F7: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:22, 29 March 2012


Name:Melanocyte - dark, donor3
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
sexNA
ageNA
cell typemelanocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number4260
catalog numberSC2205-3
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-penis-0.0259
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-lymphoma0.511
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs12570

Jaspar motifP-value
MA0002.20.109
MA0003.10.42
MA0004.18.90388e-4
MA0006.10.316
MA0007.10.719
MA0009.10.505
MA0014.10.164
MA0017.10.604
MA0018.20.0122
MA0019.10.381
MA0024.12.51528e-11
MA0025.10.27
MA0027.10.496
MA0028.11.63804e-4
MA0029.10.541
MA0030.10.343
MA0031.10.829
MA0035.20.95
MA0038.13.02638e-4
MA0039.20.0146
MA0040.10.995
MA0041.10.622
MA0042.10.598
MA0043.10.545
MA0046.10.13
MA0047.20.409
MA0048.10.866
MA0050.10.00165
MA0051.10.204
MA0052.10.237
MA0055.10.00524
MA0057.10.519
MA0058.13.26915e-6
MA0059.10.00626
MA0060.17.9507e-18
MA0061.11.08944e-4
MA0062.24.10183e-6
MA0065.20.478
MA0066.10.935
MA0067.18.9128e-4
MA0068.10.0342
MA0069.10.168
MA0070.10.00179
MA0071.10.781
MA0072.10.794
MA0073.10.861
MA0074.10.93
MA0076.15.12905e-5
MA0077.10.288
MA0078.10.448
MA0079.20.292
MA0080.25.55833e-5
MA0081.10.99
MA0083.10.00356
MA0084.10.595
MA0087.10.232
MA0088.10.0421
MA0090.10.12
MA0091.10.975
MA0092.10.442
MA0093.14.47679e-4
MA0099.20.00529
MA0100.10.186
MA0101.10.0489
MA0102.21.46295e-4
MA0103.16.76835e-4
MA0104.26.42499e-4
MA0105.11.85992e-5
MA0106.10.732
MA0107.10.00468
MA0108.20.336
MA0111.10.826
MA0112.20.00204
MA0113.10.438
MA0114.10.597
MA0115.10.157
MA0116.10.013
MA0117.10.46
MA0119.10.245
MA0122.10.733
MA0124.10.0271
MA0125.10.0137
MA0131.10.179
MA0135.10.299
MA0136.10.0261
MA0137.20.157
MA0138.20.745
MA0139.10.344
MA0140.10.515
MA0141.10.304
MA0142.10.781
MA0143.10.804
MA0144.10.0589
MA0145.10.182
MA0146.10.656
MA0147.10.0146
MA0148.10.489
MA0149.10.0262
MA0150.10.0249
MA0152.10.334
MA0153.10.536
MA0154.10.0236
MA0155.10.17
MA0156.10.952
MA0157.10.464
MA0159.10.955
MA0160.10.321
MA0162.10.476
MA0163.10.0157
MA0164.10.0451
MA0258.10.0925
MA0259.10.0216



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: CNhs12570

Novel motifP-value
10.861
100.328
1000.43
1010.555
1020.142
1030.618
1040.77
1050.811
1061.81654e-4
1070.0036
1080.35
1090.773
110.432
1100.349
1110.672
1120.307
1130.119
1140.19
1150.0664
1160.107
1170.492
1180.901
1190.184
120.969
1200.969
1210.979
1220.578
1230.731
1240.968
1250.117
1260.65
1270.929
1280.11
1290.534
130.62
1300.0782
1310.064
1320.1
1330.899
1340.674
1350.92
1360.0132
1370.952
1380.914
1392.18674e-4
140.962
1400.323
1410.894
1420.212
1430.692
1440.568
1450.469
1460.54
1470.869
1480.0371
1490.0232
150.841
1500.562
1510.434
1520.0773
1530.258
1540.616
1550.934
1560.909
1570.668
1580.63
1590.759
160.656
1600.246
1610.285
1620.707
1630.362
1640.305
1650.287
1660.33
1670.528
1680.894
1690.0875
170.405
180.844
190.477
20.259
200.516
210.36
220.919
230.00445
240.878
250.618
260.274
270.734
280.708
290.404
30.332
300.24
310.92
322.15888e-4
330.755
340.478
350.0572
360.622
370.101
380.979
390.465
40.544
400.429
410.989
420.451
430.175
440.921
450.209
460.364
470.776
480.416
490.357
50.433
500.667
510.736
520.165
530.729
540.874
550.189
560.708
570.365
580.0418
590.0414
60.0608
600.033
610.812
620.00486
630.438
640.911
650.491
660.00588
670.754
680.453
690.722
70.649
700.0411
710.149
720.371
730.3
740.737
750.258
760.335
770.281
780.129
790.495
80.727
800.838
810.391
820.0164
830.933
840.442
850.0322
860.159
870.0908
880.75
890.63
90.347
900.338
910.134
920.00316
930.11
940.87
950.371
960.474
970.549
980.888
990.809



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: CNhs12570


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)
0000055 (non-terminally differentiated cell)
0000066 (epithelial cell)
0000075 (columnar/cuboidal epithelial cell)
0000133 (neurectodermal cell)
0000147 (pigment cell)
0000148 (melanocyte)
0000219 (motile cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000325 (stuff accumulating cell)
0000333 (migratory neural crest cell)
0000541 (melanoblast)
0000548 (animal cell)
0000710 (neurecto-epithelial cell)
0002077 (ecto-epithelial cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002566 (dark melanocyte)

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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