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FF:11351-117H1: 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 16:48, 29 March 2012


Name:Melanocyte - light, donor2
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 number1607
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-penis-0.0844
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-lymphoma-0.0376
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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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: CNhs11383

Jaspar motifP-value
MA0002.20.217
MA0003.10.245
MA0004.11.77055e-5
MA0006.10.681
MA0007.10.0558
MA0009.10.505
MA0014.10.279
MA0017.10.628
MA0018.20.914
MA0019.10.141
MA0024.10.456
MA0025.10.408
MA0027.10.41
MA0028.10.756
MA0029.10.802
MA0030.10.778
MA0031.10.81
MA0035.20.0194
MA0038.10.0156
MA0039.20.0236
MA0040.10.521
MA0041.10.306
MA0042.10.813
MA0043.10.0366
MA0046.10.516
MA0047.20.919
MA0048.10.949
MA0050.10.668
MA0051.10.679
MA0052.10.0198
MA0055.10.00611
MA0057.10.385
MA0058.12.14797e-10
MA0059.12.30341e-4
MA0060.14.96006e-8
MA0061.10.0321
MA0062.20.38
MA0065.20.0589
MA0066.10.385
MA0067.10.00223
MA0068.10.312
MA0069.10.178
MA0070.12.20598e-5
MA0071.10.442
MA0072.10.942
MA0073.10.929
MA0074.10.0326
MA0076.10.46
MA0077.10.17
MA0078.10.993
MA0079.20.179
MA0080.20.0228
MA0081.10.539
MA0083.10.346
MA0084.10.429
MA0087.10.611
MA0088.10.134
MA0090.10.532
MA0091.10.274
MA0092.10.677
MA0093.17.09823e-6
MA0099.20.54
MA0100.10.628
MA0101.10.182
MA0102.20.0191
MA0103.10.721
MA0104.20.0104
MA0105.10.129
MA0106.10.886
MA0107.10.0531
MA0108.20.472
MA0111.10.369
MA0112.20.621
MA0113.10.746
MA0114.10.0751
MA0115.10.632
MA0116.10.554
MA0117.10.0737
MA0119.10.698
MA0122.10.859
MA0124.10.374
MA0125.10.0202
MA0131.10.324
MA0135.10.0313
MA0136.10.0463
MA0137.20.285
MA0138.20.978
MA0139.10.407
MA0140.10.1
MA0141.10.0107
MA0142.10.168
MA0143.10.648
MA0144.10.159
MA0145.10.266
MA0146.10.0031
MA0147.10.0199
MA0148.10.921
MA0149.10.0852
MA0150.10.978
MA0152.10.0889
MA0153.10.186
MA0154.10.456
MA0155.10.307
MA0156.10.152
MA0157.10.858
MA0159.10.114
MA0160.10.00964
MA0162.10.206
MA0163.10.686
MA0164.10.613
MA0258.10.186
MA0259.10.174



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: CNhs11383

Novel motifP-value
10.864
100.538
1000.533
1010.0478
1020.0388
1030.0531
1040.283
1050.976
1060.926
1070.666
1080.866
1090.022
110.682
1100.0379
1110.0649
1120.73
1130.0188
1140.571
1150.749
1160.89
1170.271
1180.873
1190.695
120.66
1200.955
1210.295
1220.163
1230.956
1240.895
1250.484
1260.794
1270.645
1280.429
1290.0298
130.367
1300.416
1310.522
1320.412
1330.351
1340.71
1350.268
1360.101
1370.714
1380.91
1390.176
140.935
1400.39
1410.095
1420.975
1430.409
1440.764
1450.672
1463.41269e-4
1470.6
1480.0113
1490.695
150.782
1500.734
1510.861
1520.283
1530.069
1540.0166
1550.654
1560.921
1570.867
1580.567
1590.843
160.377
1600.701
1610.641
1620.048
1630.726
1640.255
1650.18
1660.486
1670.17
1680.215
1690.21
170.419
180.158
190.311
20.933
200.824
210.414
220.011
230.668
240.949
250.358
260.49
270.23
280.273
290.0543
30.886
300.641
310.673
320.0868
330.304
340.236
350.438
360.884
370.66
380.312
390.799
40.601
400.0144
410.927
420.264
430.463
440.979
450.7
460.345
470.675
480.902
490.581
50.6
500.364
510.913
520.797
530.112
540.626
550.447
560.587
570.45
580.128
590.268
60.933
600.823
610.677
620.0293
630.51
640.363
650.0683
660.00564
670.664
680.151
690.709
70.946
700.822
710.729
720.949
730.00748
740.189
750.528
760.887
770.412
780.21
790.647
80.3
800.76
810.856
820.998
830.277
840.151
850.351
860.782
876.4636e-4
880.267
890.506
90.324
900.0226
910.612
920.0136
930.316
940.751
950.0526
960.903
970.196
980.127
990.266



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: CNhs11383


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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