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FF:13433-144E4: 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 C32-CRL1502, day00, rep1
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
sexfemale
age12wk gestation
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-penis0.107
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-lymphoma0.587
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: CNhs13826

Jaspar motifP-value
MA0002.20.00295
MA0003.10.0596
MA0004.10.966
MA0006.10.474
MA0007.10.848
MA0009.10.401
MA0014.10.178
MA0017.10.0264
MA0018.20.0852
MA0019.10.915
MA0024.11.2888e-5
MA0025.10.601
MA0027.10.252
MA0028.10.0952
MA0029.10.754
MA0030.10.358
MA0031.10.325
MA0035.20.812
MA0038.10.00339
MA0039.20.024
MA0040.10.42
MA0041.10.0637
MA0042.10.413
MA0043.10.352
MA0046.10.319
MA0047.20.0709
MA0048.10.431
MA0050.15.90262e-5
MA0051.10.00551
MA0052.10.0847
MA0055.10.281
MA0057.10.333
MA0058.10.969
MA0059.10.958
MA0060.11.12106e-13
MA0061.10.0274
MA0062.20.489
MA0065.20.578
MA0066.10.256
MA0067.10.229
MA0068.10.00452
MA0069.10.537
MA0070.10.306
MA0071.10.978
MA0072.10.964
MA0073.10.888
MA0074.10.774
MA0076.10.129
MA0077.10.0763
MA0078.10.935
MA0079.20.31
MA0080.23.07425e-12
MA0081.10.0951
MA0083.10.0359
MA0084.10.964
MA0087.10.714
MA0088.10.932
MA0090.10.801
MA0091.10.0267
MA0092.10.0822
MA0093.10.895
MA0099.21.02161e-12
MA0100.10.941
MA0101.10.148
MA0102.20.00962
MA0103.10.114
MA0104.20.892
MA0105.10.00585
MA0106.10.856
MA0107.10.0795
MA0108.21.41154e-4
MA0111.10.763
MA0112.21.77431e-5
MA0113.10.0209
MA0114.10.289
MA0115.10.909
MA0116.10.00962
MA0117.10.624
MA0119.10.00269
MA0122.10.779
MA0124.10.343
MA0125.10.127
MA0131.10.371
MA0135.10.904
MA0136.19.28575e-10
MA0137.20.185
MA0138.20.897
MA0139.10.782
MA0140.10.174
MA0141.10.388
MA0142.11.03788e-12
MA0143.17.21618e-5
MA0144.10.041
MA0145.10.173
MA0146.10.192
MA0147.10.86
MA0148.10.0242
MA0149.10.19
MA0150.19.18099e-4
MA0152.10.687
MA0153.10.398
MA0154.10.016
MA0155.10.967
MA0156.11.38535e-4
MA0157.10.168
MA0159.10.0904
MA0160.10.218
MA0162.10.914
MA0163.16.14518e-4
MA0164.10.827
MA0258.10.0288
MA0259.10.899



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: CNhs13826

Novel motifP-value
10.135
100.143
1000.63
1010.682
1020.66
1030.0581
1040.643
1050.171
1060.0485
1070.335
1080.94
1090.288
110.19
1100.212
1110.0675
1120.25
1130.122
1140.0435
1150.209
1160.731
1170.322
1180.51
1190.216
120.977
1200.863
1210.675
1220.789
1230.856
1240.232
1250.656
1260.413
1270.303
1280.34
1290.217
130.768
1300.628
1310.72
1320.929
1330.0478
1340.425
1350.00142
1360.0767
1370.466
1380.18
1390.0187
140.661
1400.0261
1410.328
1420.334
1430.00462
1440.609
1450.62
1460.457
1470.679
1480.0381
1490.0153
150.0885
1500.675
1510.0885
1520.69
1530.151
1540.56
1550.949
1560.387
1570.556
1580.164
1590.221
160.392
1600.447
1610.666
1620.349
1630.428
1640.335
1650.415
1660.871
1670.147
1680.19
1697.60522e-4
170.172
180.134
190.138
20.416
200.904
210.746
220.109
230.0116
240.765
250.439
260.587
270.272
280.911
290.547
30.157
300.851
310.716
320.0922
330.954
340.509
350.23
360.506
370.225
380.261
390.804
40.552
400.909
410.0909
420.323
430.0988
440.931
450.386
460.0605
470.884
480.758
490.0887
50.08
500.928
510.401
520.368
530.453
540.32
550.0478
560.579
570.534
580.0608
590.161
60.879
600.0563
610.953
620.0176
630.178
640.467
650.0537
660.529
670.334
680.935
690.827
70.354
700.0141
710.0881
720.445
730.301
740.357
750.205
760.582
770.22
780.568
790.151
80.137
800.06
810.331
820.124
830.654
840.522
850.036
860.601
870.0923
880.756
890.0763
90.102
900.325
910.18
920.031
930.123
940.0817
950.961
960.0322
970.566
980.169
990.626



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: CNhs13826


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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