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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101575
|fonse_cell_line=FF:0101575
|fonse_cell_line_closure=FF:0101575
|fonse_cell_line_closure=FF:0101575

Revision as of 16:54, 29 March 2012


Name:choriocarcinoma cell line:T3M-3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuechorioamniotic membrane
dev stageNA
sexunknown
agefetal
cell typetrophoblast cell
cell lineT3M-3
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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-penis0.205
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-lymphoma0.36
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs11820

Jaspar motifP-value
MA0002.20.00445
MA0003.10.575
MA0004.10.0656
MA0006.10.946
MA0007.10.903
MA0009.10.849
MA0014.10.092
MA0017.10.451
MA0018.20.643
MA0019.10.101
MA0024.10.00346
MA0025.10.935
MA0027.10.99
MA0028.12.74789e-5
MA0029.10.167
MA0030.10.849
MA0031.10.746
MA0035.27.36271e-5
MA0038.10.00493
MA0039.24.86656e-4
MA0040.10.818
MA0041.10.32
MA0042.10.504
MA0043.10.731
MA0046.10.754
MA0047.20.311
MA0048.10.361
MA0050.11.55646e-11
MA0051.13.39712e-7
MA0052.10.00427
MA0055.11.14058e-4
MA0057.10.662
MA0058.10.0123
MA0059.10.0237
MA0060.14.73569e-6
MA0061.19.11071e-4
MA0062.24.73568e-4
MA0065.20.0423
MA0066.10.864
MA0067.10.275
MA0068.10.969
MA0069.10.815
MA0070.10.62
MA0071.10.128
MA0072.10.676
MA0073.10.757
MA0074.10.739
MA0076.18.5678e-5
MA0077.10.199
MA0078.10.688
MA0079.20.998
MA0080.24.15394e-6
MA0081.10.00644
MA0083.17.40669e-4
MA0084.10.393
MA0087.10.839
MA0088.10.2
MA0090.10.00123
MA0091.10.195
MA0092.10.152
MA0093.10.0462
MA0099.21.69059e-4
MA0100.10.901
MA0101.10.0195
MA0102.20.747
MA0103.11.14315e-6
MA0104.20.0263
MA0105.10.00383
MA0106.10.667
MA0107.16.86988e-4
MA0108.20.0207
MA0111.10.825
MA0112.20.64
MA0113.10.754
MA0114.10.00913
MA0115.10.363
MA0116.10.16
MA0117.10.633
MA0119.10.296
MA0122.10.865
MA0124.10.207
MA0125.10.831
MA0131.10.354
MA0135.10.463
MA0136.14.85115e-4
MA0137.20.345
MA0138.20.052
MA0139.10.179
MA0140.10.00325
MA0141.10.887
MA0142.10.173
MA0143.10.502
MA0144.10.503
MA0145.10.946
MA0146.10.625
MA0147.10.0213
MA0148.10.905
MA0149.10.353
MA0150.10.461
MA0152.10.213
MA0153.10.441
MA0154.10.241
MA0155.10.489
MA0156.10.083
MA0157.10.42
MA0159.10.933
MA0160.10.387
MA0162.10.855
MA0163.10.124
MA0164.10.956
MA0258.10.925
MA0259.10.111



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: CNhs11820

Novel motifP-value
10.803
100.937
1000.0656
1010.706
1020.518
1030.101
1040.17
1050.55
1060.0194
1070.672
1080.716
1090.0812
110.824
1100.271
1110.672
1120.247
1130.14
1140.314
1150.886
1160.569
1170.271
1180.366
1190.875
120.773
1200.735
1210.955
1220.811
1230.0186
1240.956
1250.649
1260.991
1270.621
1280.168
1290.643
130.00889
1300.923
1310.238
1320.907
1336.42448e-4
1340.767
1350.0195
1360.0347
1370.0302
1380.92
1390.565
140.861
1400.569
1410.123
1420.25
1430.0291
1440.0419
1450.891
1460.937
1470.312
1480.109
1490.528
150.743
1500.258
1510.198
1520.899
1530.439
1540.856
1550.307
1560.625
1570.802
1580.597
1590.914
160.65
1600.752
1610.529
1620.394
1630.359
1640.796
1650.181
1660.0142
1670.611
1680.0341
1690.913
170.445
180.77
190.384
20.34
200.356
210.6
220.692
230.127
240.85
250.478
260.976
270.473
280.918
290.606
30.987
300.722
310.417
320.142
330.936
340.59
350.214
360.0646
370.707
380.528
390.124
40.375
400.0359
410.0475
420.481
430.384
440.915
450.937
460.501
470.482
480.525
490.637
50.468
500.514
510.919
520.708
530.627
540.948
550.943
560.664
570.0418
580.994
590.0799
60.102
600.363
610.404
620.598
630.655
640.457
650.763
660.0519
670.611
680.1
690.604
70.205
700.142
710.147
720.119
730.974
740.225
750.976
760.468
770.781
780.274
790.151
80.526
800.0908
810.456
820.57
830.216
840.953
850.0814
860.246
870.561
880.641
890.0542
90.148
900.709
910.0684
920.285
930.815
940.825
950.068
960.366
970.444
980.66
990.662



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: CNhs11820


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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