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FF:12627-134E8: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100669
|fonse_cell_line=FF:0100669
|fonse_cell_line_closure=FF:0100669
|fonse_cell_line_closure=FF:0100669

Revision as of 17:25, 29 March 2012


Name:H9 Embryoid body cells, melanocytic induction, day00, biol_rep1 (H9EB-1 d0)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageNA
sexfemale
ageNA
cell typestem cell
cell lineH9
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-penis-0.0455
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-lymphoma0.556
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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: CNhs12822

Jaspar motifP-value
MA0002.21.00867e-5
MA0003.10.236
MA0004.10.686
MA0006.10.69
MA0007.10.623
MA0009.10.609
MA0014.10.612
MA0017.10.68
MA0018.20.428
MA0019.10.268
MA0024.16.15371e-5
MA0025.10.387
MA0027.10.586
MA0028.10.274
MA0029.10.496
MA0030.10.896
MA0031.10.583
MA0035.20.243
MA0038.15.36949e-4
MA0039.20.0406
MA0040.10.872
MA0041.10.937
MA0042.10.922
MA0043.10.825
MA0046.10.0222
MA0047.20.27
MA0048.10.889
MA0050.19.16806e-10
MA0051.14.83347e-5
MA0052.10.219
MA0055.10.259
MA0057.10.515
MA0058.10.706
MA0059.10.797
MA0060.11.23031e-13
MA0061.10.00667
MA0062.20.722
MA0065.20.826
MA0066.10.516
MA0067.10.148
MA0068.10.00927
MA0069.10.422
MA0070.10.012
MA0071.10.973
MA0072.10.998
MA0073.10.859
MA0074.10.934
MA0076.10.27
MA0077.10.186
MA0078.10.892
MA0079.20.136
MA0080.28.2981e-12
MA0081.10.0383
MA0083.10.308
MA0084.10.645
MA0087.10.637
MA0088.10.297
MA0090.10.465
MA0091.10.0269
MA0092.10.0573
MA0093.10.57
MA0099.22.50533e-10
MA0100.10.869
MA0101.10.0468
MA0102.20.00202
MA0103.10.18
MA0104.20.853
MA0105.12.67153e-4
MA0106.10.295
MA0107.10.0322
MA0108.21.26293e-13
MA0111.10.625
MA0112.28.11795e-5
MA0113.10.112
MA0114.10.979
MA0115.10.389
MA0116.10.00422
MA0117.10.682
MA0119.13.44338e-4
MA0122.10.864
MA0124.10.975
MA0125.10.00276
MA0131.10.938
MA0135.10.0804
MA0136.11.48814e-10
MA0137.20.502
MA0138.20.869
MA0139.10.875
MA0140.10.851
MA0141.10.463
MA0142.13.4138e-11
MA0143.11.91218e-4
MA0144.10.0646
MA0145.10.147
MA0146.10.461
MA0147.10.764
MA0148.10.0785
MA0149.10.0223
MA0150.11.7857e-4
MA0152.10.572
MA0153.10.0409
MA0154.10.0293
MA0155.10.477
MA0156.11.58592e-4
MA0157.10.207
MA0159.10.101
MA0160.10.246
MA0162.10.89
MA0163.12.53618e-5
MA0164.10.707
MA0258.10.0582
MA0259.10.452



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: CNhs12822

Novel motifP-value
10.0626
100.0107
1000.905
1010.271
1020.834
1030.192
1040.718
1050.167
1060.033
1070.362
1080.667
1090.216
110.096
1100.265
1110.0103
1120.328
1130.502
1140.00844
1150.258
1160.858
1170.101
1180.701
1190.171
120.972
1200.409
1210.966
1220.885
1230.0108
1240.15
1250.563
1260.68
1270.555
1280.494
1290.464
130.595
1300.147
1310.748
1320.952
1330.143
1340.501
1350.0508
1360.206
1370.248
1380.21
1390.0103
140.573
1400.0251
1410.692
1420.965
1430.00507
1440.746
1450.314
1460.42
1470.775
1480.00294
1490.0547
150.0459
1500.498
1510.0629
1520.612
1530.382
1540.126
1550.992
1560.595
1570.534
1580.444
1590.822
160.388
1600.424
1610.556
1620.425
1630.418
1640.171
1650.166
1660.773
1670.0116
1680.364
1690.00167
170.28
180.249
190.237
20.73
200.875
210.507
220.275
230.0518
240.716
250.376
260.119
270.622
280.671
290.662
30.0562
300.584
310.973
320.131
330.709
340.912
350.297
360.0423
370.218
380.321
390.578
40.837
400.739
410.127
420.208
430.113
440.838
450.798
460.0511
470.479
480.426
490.072
50.0872
500.908
510.748
520.553
530.168
540.473
550.0121
560.602
570.273
580.0932
590.466
60.646
600.125
610.823
620.0314
630.1
640.256
650.138
660.623
670.224
680.413
690.703
70.376
700.00717
710.0329
720.493
730.124
740.154
750.207
760.322
770.352
780.506
790.343
80.0984
800.363
810.245
820.0695
830.352
840.851
850.0688
860.304
870.545
880.933
890.159
90.296
900.103
910.165
920.0432
930.267
940.0517
950.785
960.0172
970.641
980.207
990.481



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: CNhs12822


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)
0000034 (stem 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)
0002322 (embryonic stem cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0001062 (anatomical entity)

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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