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FF:11841-124H5: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120,FF:0101555
|fonse_cell_line=FF:0101120,FF:0101555
|fonse_cell_line_closure=FF:0101120,FF:0101555
|fonse_cell_line_closure=FF:0101120,FF:0101555

Revision as of 17:29, 29 March 2012


Name:serous adenocarcinoma cell line:SK-OV-3-R, biol_rep1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal precursor cell
cell lineNA
companyNA
collaborationClaudio Schneider LNCIB
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-TRIzol-ethanol-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
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-lymphoma0.389
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs13099

Jaspar motifP-value
MA0002.20.199
MA0003.10.138
MA0004.10.548
MA0006.10.274
MA0007.10.0327
MA0009.10.938
MA0014.10.0434
MA0017.10.463
MA0018.20.00573
MA0019.10.849
MA0024.10.257
MA0025.10.264
MA0027.10.639
MA0028.10.791
MA0029.10.385
MA0030.10.0994
MA0031.10.357
MA0035.20.874
MA0038.10.811
MA0039.20.196
MA0040.10.468
MA0041.10.646
MA0042.10.875
MA0043.13.49847e-4
MA0046.10.158
MA0047.20.259
MA0048.10.524
MA0050.12.29659e-6
MA0051.10.0152
MA0052.10.00985
MA0055.10.261
MA0057.10.432
MA0058.10.193
MA0059.10.243
MA0060.10.00196
MA0061.10.459
MA0062.20.465
MA0065.20.0594
MA0066.10.111
MA0067.10.0154
MA0068.15.65768e-4
MA0069.10.792
MA0070.10.934
MA0071.10.31
MA0072.10.676
MA0073.10.482
MA0074.10.328
MA0076.10.446
MA0077.10.3
MA0078.10.221
MA0079.20.159
MA0080.28.18792e-5
MA0081.10.0511
MA0083.10.852
MA0084.10.917
MA0087.10.245
MA0088.10.0128
MA0090.10.829
MA0091.10.963
MA0092.10.509
MA0093.10.418
MA0099.23.76571e-13
MA0100.10.256
MA0101.10.5
MA0102.20.0651
MA0103.10.273
MA0104.20.922
MA0105.12.96607e-5
MA0106.10.0696
MA0107.10.63
MA0108.20.411
MA0111.10.348
MA0112.20.0121
MA0113.10.723
MA0114.10.325
MA0115.10.723
MA0116.13.89612e-4
MA0117.10.555
MA0119.10.0218
MA0122.10.72
MA0124.10.479
MA0125.10.758
MA0131.10.683
MA0135.10.154
MA0136.19.4705e-4
MA0137.20.877
MA0138.20.375
MA0139.10.236
MA0140.10.915
MA0141.10.0198
MA0142.10.284
MA0143.10.42
MA0144.10.621
MA0145.10.485
MA0146.10.948
MA0147.10.401
MA0148.10.841
MA0149.10.0206
MA0150.10.0388
MA0152.10.0724
MA0153.10.0916
MA0154.10.0753
MA0155.10.908
MA0156.10.0192
MA0157.10.914
MA0159.10.0911
MA0160.10.366
MA0162.10.127
MA0163.10.00218
MA0164.10.785
MA0258.10.0601
MA0259.10.236



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: CNhs13099

Novel motifP-value
10.00923
100.109
1000.0303
1010.385
1020.845
1030.157
1040.735
1050.783
1060.427
1070.572
1080.659
1090.0663
110.126
1100.239
1110.358
1120.229
1130.421
1140.158
1150.646
1160.552
1170.137
1180.54
1190.334
120.627
1200.0527
1210.479
1220.9
1231
1240.0128
1250.113
1260.672
1270.521
1280.86
1290.317
130.106
1300.827
1310.249
1320.14
1330.0176
1340.544
1350.084
1360.64
1370.811
1380.337
1390.843
140.906
1400.184
1410.155
1420.678
1430.00472
1440.529
1450.57
1460.832
1470.151
1480.421
1490.433
150.0144
1500.538
1510.564
1520.316
1530.87
1540.998
1550.687
1560.0388
1570.593
1580.376
1590.252
160.109
1600.156
1610.604
1620.37
1630.484
1640.231
1650.696
1660.563
1670.0511
1680.749
1690.097
170.633
180.1
190.563
20.806
200.91
210.918
220.665
230.317
240.213
250.27
260.0193
270.507
280.929
290.11
30.13
300.947
310.864
320.924
330.0152
340.176
350.388
360.0223
370.164
380.411
390.686
40.144
400.027
410.849
420.176
430.176
440.0805
450.717
460.021
470.132
480.142
490.103
50.168
500.881
510.682
520.818
530.629
540.88
550.581
560.32
570.172
580.815
590.374
60.656
600.522
610.366
620.278
630.352
640.114
650.818
661.66553e-4
670.612
680.712
690.408
70.21
700.525
710.0558
720.988
730.871
740.397
750.23
760.611
770.378
780.453
790.826
80.0187
800.947
810.172
820.351
830.0303
840.618
850.45
860.359
870.239
880.785
890.2
90.991
900.516
910.317
920.794
930.407
940.0308
950.714
960.57
970.792
980.162
990.312



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: CNhs13099


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000066 (epithelial cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000499 (stromal cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002076 (endo-epithelial cell)
0002149 (epithelial cell of uterus)
0002255 (stromal cell of endometrium)
0002320 (connective tissue cell)
0002321 (embryonic cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
120 (female reproductive organ cancer)
14566 (disease of cellular proliferation)
162 (cancer)
193 (reproductive organ cancer)
299 (adenocarcinoma)
3001 (female reproductive endometrioid cancer)
305 (carcinoma)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000995 (uterus)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0003975 (internal female genitalia)
0004120 (mesoderm-derived structure)
0004175 (internal genitalia)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005795 (embryonic uterus)
0007023 (adult organism)

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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