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FF:13469-144I4: 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 17:40, 29 March 2012


Name:Myoblast differentiation to myotubes, day00, control donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskeletal muscle
dev stageNA
sexfemale
age3 years old
cell typemyoblast
cell lineNA
companyNA
collaborationBeatrice Bodega/Valerio Orlando
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-penis-0.117
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-lymphoma0.353
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs13847

Jaspar motifP-value
MA0002.20.251
MA0003.10.406
MA0004.10.573
MA0006.10.218
MA0007.10.404
MA0009.10.12
MA0014.10.229
MA0017.10.158
MA0018.20.114
MA0019.10.906
MA0024.10.0331
MA0025.10.409
MA0027.10.942
MA0028.11.10719e-5
MA0029.10.214
MA0030.10.143
MA0031.10.0604
MA0035.20.0935
MA0038.10.436
MA0039.20.0336
MA0040.10.432
MA0041.10.24
MA0042.10.279
MA0043.18.10999e-4
MA0046.10.387
MA0047.20.384
MA0048.10.423
MA0050.10.00135
MA0051.10.0943
MA0052.10.489
MA0055.10.0608
MA0057.10.903
MA0058.10.651
MA0059.10.921
MA0060.10.402
MA0061.10.00993
MA0062.24.41049e-12
MA0065.20.0107
MA0066.10.4
MA0067.10.097
MA0068.10.0664
MA0069.10.767
MA0070.10.668
MA0071.10.694
MA0072.10.322
MA0073.10.748
MA0074.10.503
MA0076.12.16801e-7
MA0077.10.624
MA0078.10.56
MA0079.20.497
MA0080.26.69715e-6
MA0081.10.00767
MA0083.18.40915e-4
MA0084.10.253
MA0087.10.989
MA0088.10.724
MA0090.12.51662e-4
MA0091.10.15
MA0092.10.611
MA0093.10.64
MA0099.21.82844e-6
MA0100.10.347
MA0101.10.078
MA0102.20.149
MA0103.12.26851e-5
MA0104.20.0899
MA0105.10.0594
MA0106.10.723
MA0107.10.0334
MA0108.20.0482
MA0111.10.711
MA0112.20.138
MA0113.10.903
MA0114.10.0989
MA0115.10.0775
MA0116.10.00594
MA0117.10.834
MA0119.10.345
MA0122.10.689
MA0124.10.348
MA0125.10.719
MA0131.10.0591
MA0135.10.145
MA0136.16.43485e-7
MA0137.20.15
MA0138.20.874
MA0139.10.195
MA0140.10.837
MA0141.10.343
MA0142.10.26
MA0143.10.284
MA0144.10.0774
MA0145.10.8
MA0146.10.0279
MA0147.10.091
MA0148.10.616
MA0149.10.86
MA0150.10.851
MA0152.15.93902e-4
MA0153.10.911
MA0154.10.0207
MA0155.10.259
MA0156.12.78593e-6
MA0157.10.196
MA0159.10.0121
MA0160.10.626
MA0162.10.755
MA0163.10.00446
MA0164.10.237
MA0258.10.0219
MA0259.10.554



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: CNhs13847

Novel motifP-value
10.741
100.149
1000.0269
1010.892
1020.358
1030.102
1040.329
1050.881
1060.376
1070.113
1080.955
1090.252
110.741
1100.805
1110.835
1120.0881
1130.388
1140.752
1150.102
1160.547
1170.0842
1180.0107
1190.865
120.46
1200.396
1211
1220.477
1230.451
1240.286
1250.554
1260.934
1270.864
1280.666
1290.534
130.0604
1309.96202e-4
1310.993
1320.0717
1330.743
1340.546
1350.388
1360.112
1370.974
1380.929
1390.0436
140.931
1400.292
1410.284
1420.309
1430.233
1440.966
1450.421
1460.0881
1470.0321
1480.661
1490.927
150.521
1500.747
1510.655
1520.603
1530.998
1540.847
1550.0792
1560.468
1570.193
1580.806
1590.804
160.841
1600.433
1610.0473
1620.0733
1630.658
1640.0045
1650.916
1660.512
1670.825
1680.151
1690.395
170.294
180.885
190.892
20.311
200.091
210.373
220.971
230.202
240.459
250.843
260.772
270.933
280.601
290.0254
30.131
300.214
310.544
320.994
330.227
340.679
350.578
360.134
370.0297
380.908
390.439
40.882
400.0264
410.399
420.723
430.966
440.0869
450.733
460.629
470.171
480.119
490.786
50.509
500.661
510.582
520.982
530.449
540.279
550.0687
560.524
570.41
580.534
590.334
60.115
600.518
610.525
620.629
630.843
640.353
650.659
660.09
670.538
680.782
690.279
70.915
700.392
710.162
720.576
730.394
740.421
750.00537
760.328
770.575
780.0911
790.619
80.972
800.0605
810.861
820.205
830.554
840.541
850.426
860.942
870.764
880.793
890.965
90.0834
900.0251
910.921
920.695
930.446
940.462
950.268
960.387
970.206
980.128
990.49



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: CNhs13847


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

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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