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FF:13425-144D5: 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:iPS differentiation to neuron, control donor C11-CRL2429, day00, rep2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
agenewborn
cell typefibroblast-derived iPS
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
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-penis0.105
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-lymphoma0.585
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs13822

Jaspar motifP-value
MA0002.20.00348
MA0003.10.0666
MA0004.10.91
MA0006.10.317
MA0007.10.988
MA0009.10.985
MA0014.10.133
MA0017.10.0544
MA0018.20.0773
MA0019.10.911
MA0024.11.9446e-5
MA0025.10.305
MA0027.10.341
MA0028.10.11
MA0029.10.733
MA0030.10.273
MA0031.10.188
MA0035.20.994
MA0038.10.00281
MA0039.20.0148
MA0040.10.336
MA0041.10.0718
MA0042.10.498
MA0043.10.249
MA0046.10.17
MA0047.20.0848
MA0048.10.333
MA0050.18.89454e-6
MA0051.10.00229
MA0052.10.163
MA0055.10.173
MA0057.10.361
MA0058.10.92
MA0059.10.988
MA0060.17.73118e-15
MA0061.10.00424
MA0062.20.686
MA0065.20.928
MA0066.10.263
MA0067.10.239
MA0068.10.0047
MA0069.10.652
MA0070.10.282
MA0071.10.829
MA0072.10.999
MA0073.10.965
MA0074.10.657
MA0076.10.272
MA0077.10.0993
MA0078.10.901
MA0079.20.401
MA0080.27.98192e-12
MA0081.10.0627
MA0083.10.0546
MA0084.10.715
MA0087.10.607
MA0088.10.739
MA0090.10.974
MA0091.10.0236
MA0092.10.16
MA0093.10.78
MA0099.24.87729e-14
MA0100.10.978
MA0101.10.0661
MA0102.20.00286
MA0103.10.0819
MA0104.20.844
MA0105.10.00119
MA0106.10.629
MA0107.10.0158
MA0108.21.31306e-6
MA0111.10.859
MA0112.23.67939e-5
MA0113.10.00991
MA0114.10.499
MA0115.10.672
MA0116.10.0145
MA0117.10.82
MA0119.10.00456
MA0122.10.721
MA0124.10.587
MA0125.10.183
MA0131.10.565
MA0135.10.924
MA0136.11.81175e-9
MA0137.20.0911
MA0138.20.73
MA0139.10.402
MA0140.10.349
MA0141.10.477
MA0142.11.27152e-13
MA0143.16.02631e-6
MA0144.10.0334
MA0145.10.307
MA0146.10.093
MA0147.10.848
MA0148.10.0567
MA0149.10.342
MA0150.13.80006e-4
MA0152.10.467
MA0153.10.686
MA0154.10.0164
MA0155.10.891
MA0156.17.61585e-5
MA0157.10.152
MA0159.10.107
MA0160.10.17
MA0162.10.826
MA0163.19.87571e-4
MA0164.10.861
MA0258.10.0215
MA0259.10.96



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: CNhs13822

Novel motifP-value
10.102
100.15
1000.494
1010.638
1020.635
1030.0403
1040.601
1050.232
1060.0499
1070.557
1080.966
1090.254
110.191
1100.307
1110.0256
1120.214
1130.141
1140.0237
1150.493
1160.84
1170.33
1180.647
1190.209
120.907
1200.91
1210.451
1220.787
1230.796
1240.223
1250.787
1260.484
1270.308
1280.372
1290.252
130.882
1300.42
1310.692
1320.818
1330.069
1340.481
1357.36777e-4
1360.0566
1370.44
1380.207
1390.0182
140.816
1400.0777
1410.36
1420.301
1430.00566
1440.629
1450.553
1460.51
1470.709
1480.0198
1490.00956
150.0911
1500.64
1510.0644
1520.782
1530.169
1540.534
1550.854
1560.414
1570.728
1580.169
1590.167
160.384
1600.444
1610.884
1620.536
1630.643
1640.211
1650.664
1660.576
1670.094
1680.25
1690.00131
170.14
180.137
190.18
20.348
200.864
210.785
220.0889
230.0141
240.614
250.458
260.834
270.243
280.929
290.674
30.138
300.891
310.798
320.0469
330.837
340.52
350.249
360.709
370.236
380.254
390.827
40.698
400.71
410.098
420.305
430.111
440.799
450.377
460.0532
470.829
480.677
490.0884
50.112
500.99
510.44
520.461
530.445
540.345
550.0511
560.517
570.589
580.0967
590.188
60.76
600.073
610.934
620.0277
630.127
640.366
650.0837
660.513
670.257
680.871
690.716
70.52
700.0115
710.079
720.514
730.272
740.371
750.133
760.471
770.237
780.704
790.107
80.206
800.0645
810.331
820.134
830.639
840.495
850.0422
860.518
870.0782
880.828
890.0243
90.0993
900.349
910.176
920.0236
930.114
940.0909
950.948
960.0474
970.659
980.241
990.576



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: CNhs13822


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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