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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000039,CL:0000144,CL:0000255,CL:0000548,CL:0000586
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000039,CL:0000144,CL:0000255,CL:0000548,CL:0000586
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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 16:58, 29 March 2012


Name:choriocarcinoma cell line:SCH
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuestomach
dev stageNA
sexmale
age46
cell typetrophoblast cell
cell lineSCH
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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-penis0.355
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-lymphoma0.309
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs11875

Jaspar motifP-value
MA0002.20.00211
MA0003.10.379
MA0004.10.135
MA0006.10.822
MA0007.10.769
MA0009.10.98
MA0014.10.136
MA0017.10.148
MA0018.20.477
MA0019.10.286
MA0024.10.0567
MA0025.10.985
MA0027.10.729
MA0028.10.0109
MA0029.10.14
MA0030.10.552
MA0031.10.376
MA0035.23.17013e-6
MA0038.10.0163
MA0039.23.78123e-4
MA0040.10.576
MA0041.10.181
MA0042.10.381
MA0043.10.453
MA0046.10.769
MA0047.20.646
MA0048.10.0711
MA0050.17.04488e-6
MA0051.15.88796e-4
MA0052.10.0246
MA0055.17.94296e-5
MA0057.10.448
MA0058.10.0809
MA0059.10.137
MA0060.11.45373e-7
MA0061.10.00589
MA0062.20.129
MA0065.26.05703e-4
MA0066.10.725
MA0067.10.279
MA0068.10.467
MA0069.10.503
MA0070.10.835
MA0071.10.259
MA0072.10.721
MA0073.10.971
MA0074.10.73
MA0076.10.0182
MA0077.10.569
MA0078.10.142
MA0079.20.965
MA0080.21.60847e-8
MA0081.10.00545
MA0083.14.06458e-4
MA0084.10.0469
MA0087.10.231
MA0088.10.0695
MA0090.12.62396e-5
MA0091.10.0211
MA0092.10.306
MA0093.10.125
MA0099.22.59725e-8
MA0100.10.798
MA0101.10.0195
MA0102.20.412
MA0103.14.93412e-6
MA0104.20.158
MA0105.10.172
MA0106.10.563
MA0107.14.7827e-4
MA0108.20.0179
MA0111.10.974
MA0112.20.759
MA0113.10.667
MA0114.17.64128e-4
MA0115.10.0872
MA0116.10.434
MA0117.10.935
MA0119.10.075
MA0122.10.605
MA0124.10.825
MA0125.10.924
MA0131.10.662
MA0135.10.37
MA0136.13.28667e-7
MA0137.20.24
MA0138.20.0922
MA0139.10.384
MA0140.10.00102
MA0141.10.635
MA0142.10.624
MA0143.10.288
MA0144.10.319
MA0145.10.771
MA0146.10.0719
MA0147.10.12
MA0148.10.982
MA0149.10.564
MA0150.10.165
MA0152.10.381
MA0153.10.219
MA0154.10.98
MA0155.10.983
MA0156.10.0041
MA0157.10.696
MA0159.10.592
MA0160.10.798
MA0162.10.526
MA0163.10.905
MA0164.10.359
MA0258.10.62
MA0259.10.065



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: CNhs11875

Novel motifP-value
10.63
100.703
1000.181
1010.757
1020.65
1030.212
1040.193
1050.939
1060.231
1070.237
1080.856
1090.243
110.829
1100.159
1110.817
1120.486
1130.0322
1140.559
1150.347
1160.623
1170.0393
1180.229
1190.553
120.698
1200.951
1210.741
1220.565
1230.255
1240.103
1250.593
1260.463
1270.611
1280.18
1290.698
130.00197
1300.358
1310.298
1320.386
1330.00512
1340.878
1350.00564
1360.0149
1370.172
1380.588
1390.444
140.924
1400.599
1410.123
1420.459
1430.0466
1440.162
1450.902
1460.654
1470.0671
1480.0186
1490.717
150.796
1500.946
1510.241
1520.446
1530.94
1540.366
1550.993
1560.823
1570.775
1580.4
1590.349
160.882
1600.579
1610.693
1620.342
1630.54
1640.211
1650.295
1660.0314
1670.851
1680.156
1690.511
170.421
180.346
190.705
20.485
200.139
210.665
220.658
230.159
240.481
250.812
260.391
270.256
280.786
290.441
30.944
300.925
310.551
320.194
330.343
340.785
350.389
360.298
370.714
380.786
390.277
40.881
400.0338
410.0187
420.795
430.777
440.738
450.529
460.527
470.536
480.698
490.818
50.246
500.117
510.655
520.743
530.813
540.652
550.583
560.825
570.254
580.615
590.505
60.487
600.72
610.44
620.489
630.824
640.871
650.618
660.0138
670.957
680.339
690.633
70.152
700.665
710.381
720.715
730.528
740.0598
750.13
760.159
770.839
780.0109
790.233
80.201
800.13
810.305
820.735
830.633
840.293
850.0508
860.896
870.13
880.897
890.211
90.11
900.962
910.0754
920.19
930.342
940.864
950.0065
960.819
970.847
980.866
990.689



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: CNhs11875


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)
0000039 (germ line cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000586 (germ cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
4 (disease)

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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