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FF:12641-134G4: 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 17:25, 29 March 2012


Name:Melanocyte, donor1 (MC+1)
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-penis3.910772e-4
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-lymphoma0.37
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12816

Jaspar motifP-value
MA0002.20.271
MA0003.10.958
MA0004.16.35896e-5
MA0006.10.174
MA0007.10.0359
MA0009.10.282
MA0014.10.302
MA0017.10.833
MA0018.20.708
MA0019.10.174
MA0024.11.87424e-10
MA0025.10.146
MA0027.10.883
MA0028.14.77374e-5
MA0029.10.982
MA0030.10.162
MA0031.10.247
MA0035.20.659
MA0038.10.0137
MA0039.20.0617
MA0040.10.973
MA0041.10.622
MA0042.10.628
MA0043.10.00333
MA0046.10.26
MA0047.20.484
MA0048.10.0269
MA0050.14.79486e-7
MA0051.10.00544
MA0052.10.377
MA0055.11.78543e-6
MA0057.10.0892
MA0058.18.05319e-8
MA0059.14.23202e-5
MA0060.11.22961e-6
MA0061.12.44718e-5
MA0062.22.14772e-4
MA0065.20.375
MA0066.10.225
MA0067.10.0109
MA0068.10.0498
MA0069.10.134
MA0070.10.00158
MA0071.10.633
MA0072.10.681
MA0073.10.613
MA0074.10.188
MA0076.10.001
MA0077.10.395
MA0078.10.591
MA0079.20.597
MA0080.25.08774e-5
MA0081.10.379
MA0083.10.0154
MA0084.10.417
MA0087.10.489
MA0088.10.00397
MA0090.10.553
MA0091.10.922
MA0092.10.72
MA0093.11.86456e-5
MA0099.28.86057e-4
MA0100.10.758
MA0101.10.00594
MA0102.22.75215e-6
MA0103.10.0773
MA0104.22.53429e-5
MA0105.10.00267
MA0106.10.119
MA0107.13.52916e-4
MA0108.20.00474
MA0111.10.869
MA0112.20.857
MA0113.10.861
MA0114.10.334
MA0115.10.856
MA0116.10.459
MA0117.10.178
MA0119.10.91
MA0122.10.721
MA0124.10.151
MA0125.10.0565
MA0131.10.861
MA0135.10.0774
MA0136.17.87767e-4
MA0137.20.115
MA0138.20.559
MA0139.10.85
MA0140.10.609
MA0141.10.0215
MA0142.10.599
MA0143.10.953
MA0144.10.282
MA0145.10.201
MA0146.10.32
MA0147.11.14017e-4
MA0148.10.626
MA0149.10.0426
MA0150.10.00118
MA0152.10.827
MA0153.10.652
MA0154.10.274
MA0155.10.99
MA0156.10.397
MA0157.10.392
MA0159.10.216
MA0160.10.613
MA0162.10.413
MA0163.10.884
MA0164.10.842
MA0258.10.924
MA0259.10.00252



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: CNhs12816

Novel motifP-value
10.63
100.559
1000.105
1010.131
1020.188
1030.0407
1040.508
1050.0599
1060.00513
1070.0573
1080.775
1090.0387
110.872
1100.0428
1110.849
1120.851
1130.003
1140.233
1150.944
1160.687
1170.463
1180.172
1190.548
120.351
1200.215
1210.805
1220.821
1230.279
1240.711
1250.578
1260.598
1270.627
1280.316
1290.32
130.08
1300.364
1310.0262
1320.499
1330.555
1340.875
1350.736
1360.00259
1370.81
1380.948
1390.0068
140.456
1400.349
1410.4
1420.911
1430.578
1440.558
1450.597
1460.224
1470.428
1480.163
1490.228
150.881
1500.867
1510.568
1520.394
1530.137
1540.143
1550.828
1560.943
1570.68
1580.11
1590.371
160.462
1600.318
1610.934
1620.606
1630.478
1640.883
1650.263
1660.15
1670.946
1680.748
1690.825
170.82
180.403
190.613
20.465
200.259
210.558
220.541
230.133
240.919
250.438
260.582
270.368
280.412
290.0127
30.683
300.142
310.806
320.283
330.455
340.465
350.251
360.863
370.523
380.608
390.766
40.387
400.0909
410.989
420.147
430.693
440.0558
450.0753
460.706
470.778
480.497
490.45
50.45
500.804
510.876
520.149
530.0926
540.875
550.213
560.522
570.242
580.051
590.599
60.38
600.0975
610.775
620.033
630.936
640.751
650.865
660.037
670.228
680.384
690.936
70.634
700.341
710.971
720.251
730.398
740.556
750.614
760.0777
770.574
780.254
790.86
80.616
800.346
810.483
820.367
830.888
840.368
850.341
860.244
870.0127
880.668
890.425
90.519
900.224
910.255
920.012
930.0542
940.805
955.34884e-6
960.439
970.598
980.175
990.0804



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: CNhs12816


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)

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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