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FF:11423-118G1: 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 17:08, 29 March 2012


Name:Melanocyte - light, donor3
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 number1259
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
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-0.0608
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: CNhs12033

Jaspar motifP-value
MA0002.20.444
MA0003.10.243
MA0004.10.0105
MA0006.10.506
MA0007.10.028
MA0009.10.669
MA0014.10.937
MA0017.10.422
MA0018.20.0589
MA0019.10.287
MA0024.10.529
MA0025.10.096
MA0027.10.86
MA0028.17.15472e-5
MA0029.10.98
MA0030.10.611
MA0031.10.311
MA0035.20.66
MA0038.10.182
MA0039.20.153
MA0040.10.577
MA0041.10.337
MA0042.10.78
MA0043.16.01153e-4
MA0046.10.773
MA0047.20.935
MA0048.10.985
MA0050.13.67081e-5
MA0051.10.00169
MA0052.10.00495
MA0055.10.386
MA0057.10.64
MA0058.16.01876e-4
MA0059.10.0038
MA0060.11.72549e-4
MA0061.10.265
MA0062.21.03216e-8
MA0065.20.0197
MA0066.10.623
MA0067.10.367
MA0068.10.34
MA0069.10.818
MA0070.10.0111
MA0071.10.479
MA0072.10.428
MA0073.10.783
MA0074.10.126
MA0076.17.16165e-7
MA0077.10.176
MA0078.10.463
MA0079.20.372
MA0080.25.67402e-4
MA0081.10.0221
MA0083.10.0209
MA0084.10.769
MA0087.10.616
MA0088.10.839
MA0090.10.278
MA0091.10.00326
MA0092.10.8
MA0093.10.00365
MA0099.20.567
MA0100.10.158
MA0101.10.134
MA0102.20.166
MA0103.10.936
MA0104.20.272
MA0105.10.392
MA0106.10.159
MA0107.10.204
MA0108.21.09905e-14
MA0111.10.722
MA0112.20.026
MA0113.10.198
MA0114.10.222
MA0115.10.561
MA0116.10.736
MA0117.10.128
MA0119.10.0176
MA0122.10.326
MA0124.10.404
MA0125.10.225
MA0131.10.169
MA0135.10.00853
MA0136.13.48973e-7
MA0137.20.00465
MA0138.20.18
MA0139.10.938
MA0140.10.433
MA0141.10.0641
MA0142.10.168
MA0143.10.91
MA0144.10.249
MA0145.10.31
MA0146.10.173
MA0147.10.167
MA0148.10.37
MA0149.10.943
MA0150.10.72
MA0152.10.824
MA0153.10.695
MA0154.10.666
MA0155.10.0274
MA0156.12.56475e-5
MA0157.10.343
MA0159.10.65
MA0160.10.394
MA0162.10.197
MA0163.10.904
MA0164.10.882
MA0258.10.0107
MA0259.10.455



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: CNhs12033

Novel motifP-value
10.817
100.11
1000.45
1010.172
1020.815
1030.447
1040.419
1050.774
1060.06
1070.0518
1080.362
1090.776
110.359
1100.248
1110.538
1120.625
1130.472
1140.49
1150.274
1160.219
1170.602
1180.885
1190.7
120.305
1200.694
1210.637
1220.748
1230.422
1240.901
1250.921
1260.965
1270.415
1280.0335
1290.157
130.97
1300.698
1310.111
1320.423
1330.227
1340.602
1350.874
1360.979
1370.749
1380.25
1390.663
140.62
1400.807
1410.314
1420.529
1430.56
1440.914
1450.357
1460.0133
1470.136
1480.155
1490.414
150.763
1500.182
1510.695
1520.0935
1530.846
1540.051
1550.839
1560.943
1570.162
1580.0634
1590.402
160.299
1600.244
1610.903
1620.0434
1630.357
1640.367
1650.467
1660.486
1670.142
1680.706
1690.0988
170.177
180.0855
190.111
20.271
200.591
210.831
220.14
230.413
240.395
250.317
260.156
270.231
280.13
290.729
30.773
300.435
310.0915
320.124
330.816
340.269
350.71
360.323
370.573
380.707
390.454
40.524
400.159
410.817
420.293
430.45
440.777
450.333
460.373
470.684
480.946
490.51
50.769
500.541
510.439
520.266
530.366
540.675
550.078
560.932
570.181
580.252
590.0532
60.918
600.359
610.982
620.311
630.245
640.392
650.0321
660.287
670.616
680.819
690.383
70.667
700.356
710.722
720.617
730.0518
740.541
750.856
760.196
770.0602
780.174
790.72
80.0554
800.555
810.694
820.957
830.962
840.61
850.137
860.992
870.043
880.328
890.159
90.392
900.0944
910.808
920.462
930.509
940.994
950.585
960.713
970.424
980.41
990.0179



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: CNhs12033


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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