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FF:12837-137B2: 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 17:32, 29 March 2012


Name:Melanocyte, donor3 (MC+3)
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
sexmale
ageNA
cell typemelanocyte
cell lineNA
companyNA
collaborationSusan Zabierowski (Wistar Institute)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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-penis0.0953
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-0.0022
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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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: CNhs13406

Jaspar motifP-value
MA0002.20.286
MA0003.10.982
MA0004.12.63064e-4
MA0006.10.0632
MA0007.10.85
MA0009.10.522
MA0014.10.203
MA0017.10.764
MA0018.20.77
MA0019.10.557
MA0024.10.611
MA0025.10.0316
MA0027.10.831
MA0028.10.0359
MA0029.10.435
MA0030.10.576
MA0031.10.879
MA0035.20.75
MA0038.10.284
MA0039.20.241
MA0040.10.661
MA0041.10.346
MA0042.10.889
MA0043.10.00945
MA0046.10.114
MA0047.20.977
MA0048.10.851
MA0050.10.118
MA0051.10.0604
MA0052.10.00423
MA0055.10.0424
MA0057.10.596
MA0058.14.08324e-8
MA0059.13.95848e-4
MA0060.10.137
MA0061.13.36011e-5
MA0062.20.0867
MA0065.20.299
MA0066.10.247
MA0067.10.002
MA0068.10.325
MA0069.10.412
MA0070.10.0634
MA0071.10.91
MA0072.10.306
MA0073.10.612
MA0074.10.201
MA0076.10.177
MA0077.10.59
MA0078.10.681
MA0079.20.282
MA0080.27.21611e-6
MA0081.10.729
MA0083.10.00131
MA0084.10.66
MA0087.10.244
MA0088.10.0338
MA0090.10.174
MA0091.10.858
MA0092.10.326
MA0093.11.51823e-4
MA0099.29.56993e-11
MA0100.10.407
MA0101.10.0183
MA0102.28.31097e-4
MA0103.10.0143
MA0104.22.02017e-5
MA0105.10.0046
MA0106.10.0747
MA0107.19.64016e-4
MA0108.22.34247e-11
MA0111.10.71
MA0112.20.0843
MA0113.10.462
MA0114.10.293
MA0115.10.864
MA0116.10.031
MA0117.10.00962
MA0119.10.734
MA0122.10.905
MA0124.10.156
MA0125.10.0197
MA0131.10.928
MA0135.10.313
MA0136.11.15986e-4
MA0137.20.535
MA0138.20.725
MA0139.10.811
MA0140.10.989
MA0141.10.0667
MA0142.10.686
MA0143.10.156
MA0144.10.278
MA0145.10.375
MA0146.10.193
MA0147.19.37881e-4
MA0148.10.983
MA0149.10.197
MA0150.10.00386
MA0152.10.883
MA0153.10.722
MA0154.10.163
MA0155.10.563
MA0156.10.00481
MA0157.10.788
MA0159.10.159
MA0160.10.645
MA0162.10.291
MA0163.10.937
MA0164.10.542
MA0258.10.856
MA0259.10.0643



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: CNhs13406

Novel motifP-value
10.936
100.654
1000.471
1010.757
1020.193
1030.0264
1040.968
1050.0719
1060.00266
1070.00535
1080.741
1090.969
110.452
1100.103
1110.878
1120.615
1130.0186
1140.263
1150.634
1160.0236
1170.496
1180.343
1190.256
120.398
1200.439
1210.1
1220.724
1230.346
1240.69
1250.137
1260.442
1270.907
1280.684
1290.254
130.459
1300.831
1310.426
1320.258
1330.792
1340.632
1350.563
1360.0269
1370.678
1380.428
1390.0466
140.826
1400.44
1410.705
1420.112
1430.455
1440.509
1450.851
1460.344
1470.629
1480.316
1490.239
150.746
1500.396
1510.992
1520.271
1530.641
1540.119
1550.821
1560.899
1570.394
1580.142
1590.264
160.684
1600.743
1610.679
1620.137
1630.746
1640.759
1650.305
1660.244
1670.431
1680.841
1690.252
170.492
180.505
190.674
20.0419
200.21
210.441
220.529
230.0846
240.551
250.531
260.433
270.667
280.849
290.116
30.89
300.186
310.292
320.00567
330.585
340.605
350.52
360.837
370.297
380.864
390.775
40.159
400.233
410.502
420.265
430.316
440.246
450.232
460.918
470.575
480.464
490.273
50.592
500.867
510.988
520.246
530.31
540.898
550.22
560.748
570.121
580.0589
590.481
60.0855
600.16
610.663
620.00317
630.633
640.822
650.901
660.171
670.454
680.0189
690.991
70.765
700.861
710.514
720.67
730.558
740.867
750.85
760.304
770.371
780.327
790.768
80.878
800.647
810.526
820.86
830.558
840.828
850.934
860.849
870.0269
880.581
890.826
90.302
900.385
910.754
920.025
930.157
940.896
950.343
960.614
970.625
980.111
990.45



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: CNhs13406


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)
0000150 (glandular epithelial cell)
0000151 (secretory cell)
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)

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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