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FF:11274-116H5: 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 16:44, 29 March 2012


Name:Melanocyte - light, donor1
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 stageinfant
sexmale
ageNeonatal
cell typemelanocyte
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1097
catalog numberCA104-R10n
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-penis0.104
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-lymphoma0.0429
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: CNhs11303

Jaspar motifP-value
MA0002.20.882
MA0003.10.43
MA0004.16.38786e-6
MA0006.10.727
MA0007.10.242
MA0009.10.238
MA0014.10.261
MA0017.10.82
MA0018.20.0788
MA0019.10.0434
MA0024.10.284
MA0025.10.686
MA0027.10.42
MA0028.10.38
MA0029.10.75
MA0030.10.542
MA0031.10.813
MA0035.20.191
MA0038.10.0414
MA0039.20.0109
MA0040.10.911
MA0041.10.288
MA0042.10.939
MA0043.10.422
MA0046.10.744
MA0047.20.66
MA0048.10.532
MA0050.10.421
MA0051.10.616
MA0052.10.0142
MA0055.10.00634
MA0057.10.339
MA0058.18.80678e-9
MA0059.10.00683
MA0060.11.40372e-7
MA0061.12.03187e-4
MA0062.20.0112
MA0065.20.428
MA0066.10.802
MA0067.10.00356
MA0068.10.54
MA0069.10.43
MA0070.16.99089e-5
MA0071.10.773
MA0072.10.75
MA0073.10.999
MA0074.10.302
MA0076.10.283
MA0077.10.618
MA0078.10.871
MA0079.20.0527
MA0080.20.0121
MA0081.10.973
MA0083.10.135
MA0084.10.447
MA0087.10.416
MA0088.10.398
MA0090.10.45
MA0091.10.34
MA0092.10.221
MA0093.16.71341e-6
MA0099.20.983
MA0100.10.63
MA0101.10.00641
MA0102.27.70206e-4
MA0103.10.0493
MA0104.20.00569
MA0105.14.32971e-5
MA0106.10.344
MA0107.10.00317
MA0108.20.534
MA0111.10.465
MA0112.20.117
MA0113.10.861
MA0114.10.347
MA0115.10.76
MA0116.10.00147
MA0117.10.0542
MA0119.10.25
MA0122.10.958
MA0124.10.316
MA0125.10.0307
MA0131.10.839
MA0135.10.0371
MA0136.10.0308
MA0137.20.203
MA0138.20.717
MA0139.10.866
MA0140.10.574
MA0141.10.0691
MA0142.10.6
MA0143.10.443
MA0144.10.455
MA0145.10.559
MA0146.10.0201
MA0147.10.0315
MA0148.10.578
MA0149.10.324
MA0150.10.231
MA0152.10.252
MA0153.10.725
MA0154.10.0743
MA0155.10.503
MA0156.10.448
MA0157.10.852
MA0159.10.531
MA0160.10.0821
MA0162.10.821
MA0163.10.0696
MA0164.10.967
MA0258.10.867
MA0259.10.102



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: CNhs11303

Novel motifP-value
10.339
100.0248
1000.601
1010.112
1020.131
1030.901
1040.272
1050.943
1060.465
1070.0779
1080.772
1090.303
110.528
1100.152
1110.0895
1120.618
1130.0106
1140.164
1150.859
1160.0859
1170.876
1180.666
1190.292
120.553
1200.91
1210.699
1220.265
1230.273
1240.613
1250.155
1260.336
1270.58
1280.728
1290.561
130.907
1300.21
1310.134
1320.448
1330.869
1340.865
1350.912
1360.0253
1370.679
1380.922
1390.00152
140.967
1400.45
1410.342
1420.809
1430.933
1440.815
1450.989
1460.0244
1470.866
1480.003
1490.977
150.77
1500.53
1510.68
1520.125
1530.115
1540.0693
1550.685
1560.915
1570.536
1580.369
1590.553
160.88
1600.253
1610.355
1620.15
1630.516
1640.216
1650.2
1660.353
1670.116
1680.448
1690.566
170.769
180.638
190.632
20.512
200.402
210.49
220.204
230.224
240.814
250.109
260.696
270.77
280.567
290.465
30.347
300.613
310.613
320.0069
330.923
340.522
350.0468
360.431
370.993
380.955
390.952
40.881
400.174
410.652
420.0974
430.26
440.711
450.784
460.646
470.498
480.428
490.193
50.325
500.405
510.849
520.432
530.115
540.653
550.13
560.768
570.821
580.00808
590.837
60.858
600.235
610.523
623.51316e-4
630.878
640.918
650.641
660.0707
670.722
680.348
690.452
70.196
700.176
710.125
720.554
730.02
740.362
750.876
760.779
770.996
780.032
790.366
80.574
800.467
810.316
820.34
830.59
840.355
850.518
860.875
870.00337
880.869
890.813
90.879
900.0798
910.887
920.0173
930.574
940.183
950.222
960.322
970.122
980.833
990.174



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: CNhs11303


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)
0002567 (light 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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