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FF:12739-135I3: 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 17:29, 29 March 2012


Name:Melanocyte, donor2 (MC+2)
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
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-lymphoma0.377
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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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: CNhs13156

Jaspar motifP-value
MA0002.20.769
MA0003.10.529
MA0004.12.49125e-4
MA0006.10.707
MA0007.10.0667
MA0009.10.994
MA0014.10.281
MA0017.10.0451
MA0018.20.276
MA0019.10.88
MA0024.11.62988e-4
MA0025.10.0366
MA0027.10.869
MA0028.10.0255
MA0029.10.376
MA0030.10.0169
MA0031.10.132
MA0035.20.365
MA0038.10.201
MA0039.20.0896
MA0040.10.556
MA0041.10.914
MA0042.10.311
MA0043.12.70268e-6
MA0046.10.0371
MA0047.20.251
MA0048.10.427
MA0050.10.104
MA0051.10.485
MA0052.10.123
MA0055.11.53996e-4
MA0057.10.246
MA0058.14.18988e-7
MA0059.11.17419e-4
MA0060.10.00758
MA0061.10.163
MA0062.20.0238
MA0065.26.55967e-4
MA0066.10.0485
MA0067.10.0922
MA0068.10.0387
MA0069.10.133
MA0070.10.205
MA0071.10.482
MA0072.10.107
MA0073.10.566
MA0074.10.0953
MA0076.10.116
MA0077.10.357
MA0078.10.689
MA0079.20.894
MA0080.23.8959e-4
MA0081.10.585
MA0083.11.9787e-4
MA0084.10.99
MA0087.10.284
MA0088.10.00322
MA0090.10.468
MA0091.10.176
MA0092.10.612
MA0093.16.54174e-5
MA0099.20.00621
MA0100.10.432
MA0101.10.0434
MA0102.23.33781e-4
MA0103.10.536
MA0104.20.00398
MA0105.10.328
MA0106.10.0282
MA0107.10.00222
MA0108.22.02466e-6
MA0111.10.524
MA0112.20.0608
MA0113.10.909
MA0114.10.00517
MA0115.10.02
MA0116.10.0778
MA0117.10.232
MA0119.10.364
MA0122.10.864
MA0124.10.43
MA0125.10.193
MA0131.10.543
MA0135.10.237
MA0136.10.00392
MA0137.20.232
MA0138.20.429
MA0139.10.395
MA0140.10.546
MA0141.10.00379
MA0142.10.918
MA0143.10.727
MA0144.10.194
MA0145.10.573
MA0146.10.0259
MA0147.10.00709
MA0148.10.611
MA0149.10.0149
MA0150.10.0135
MA0152.10.981
MA0153.10.989
MA0154.10.207
MA0155.10.717
MA0156.10.164
MA0157.10.491
MA0159.10.019
MA0160.10.286
MA0162.10.165
MA0163.10.00459
MA0164.10.187
MA0258.10.0495
MA0259.10.115



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: CNhs13156

Novel motifP-value
10.0155
100.218
1000.0206
1010.897
1020.181
1030.00724
1040.441
1050.677
1060.782
1070.538
1080.382
1090.00366
110.0205
1100.00107
1110.79
1120.614
1130.0206
1140.393
1150.939
1160.523
1170.0697
1180.0763
1190.952
120.539
1200.275
1210.652
1220.903
1230.206
1240.333
1250.261
1260.748
1270.889
1280.206
1290.147
130.013
1300.458
1310.0758
1320.758
1330.246
1340.47
1350.995
1360.0246
1370.983
1380.515
1390.0314
140.644
1400.253
1410.326
1420.383
1430.551
1440.391
1450.202
1460.0256
1470.984
1480.284
1490.697
150.342
1500.883
1510.365
1520.235
1530.318
1540.326
1550.886
1560.999
1570.866
1580.124
1590.202
160.0271
1600.311
1610.852
1620.215
1630.362
1640.45
1650.588
1660.207
1670.339
1680.422
1690.1
170.251
180.15
190.514
20.599
200.37
210.457
220.18
230.438
240.635
250.72
260.121
270.353
280.839
290.00618
30.24
300.254
310.281
320.289
330.362
340.803
350.825
360.0367
370.098
380.709
390.415
40.385
400.0204
410.901
420.819
430.419
440.0468
450.6
460.0892
470.026
480.0937
490.773
50.399
500.367
510.379
520.695
530.452
540.787
550.51
560.717
570.0467
580.206
590.643
60.0287
600.99
610.116
620.291
630.17
640.158
650.573
660.0683
670.553
680.241
690.103
70.515
700.431
710.0717
720.957
730.019
740.908
750.173
760.249
770.225
780.949
790.595
80.0193
800.79
810.544
820.626
830.176
840.885
850.531
860.869
870.00222
880.951
890.168
90.898
900.00783
910.666
920.142
930.0563
940.13
950.00107
960.882
970.368
980.0452
990.0461



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: CNhs13156


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)
0000149 (visual pigment 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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