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FF:11843-124H7: 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 17:36, 29 March 2012


Name:serous adenocarcinoma cell line:SK-OV-3-R after co-culture with SOC-57-02-G, 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-penis-0.0787
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-lymphoma-0.112
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: CNhs13508

Jaspar motifP-value
MA0002.20.527
MA0003.10.191
MA0004.10.856
MA0006.10.253
MA0007.10.0122
MA0009.10.341
MA0014.10.00245
MA0017.10.753
MA0018.20.0393
MA0019.10.542
MA0024.10.00573
MA0025.10.563
MA0027.10.693
MA0028.10.331
MA0029.10.06
MA0030.10.381
MA0031.10.633
MA0035.20.494
MA0038.10.449
MA0039.23.10355e-4
MA0040.10.753
MA0041.10.51
MA0042.10.764
MA0043.10.111
MA0046.10.723
MA0047.20.648
MA0048.10.433
MA0050.10.0621
MA0051.10.456
MA0052.10.117
MA0055.10.782
MA0057.10.355
MA0058.10.73
MA0059.10.367
MA0060.10.166
MA0061.10.0905
MA0062.20.00131
MA0065.20.395
MA0066.10.424
MA0067.10.527
MA0068.12.05393e-4
MA0069.10.245
MA0070.10.815
MA0071.10.146
MA0072.10.583
MA0073.10.624
MA0074.10.0448
MA0076.10.0126
MA0077.10.164
MA0078.10.971
MA0079.20.379
MA0080.24.33007e-7
MA0081.10.00288
MA0083.10.649
MA0084.10.281
MA0087.10.55
MA0088.10.57
MA0090.10.667
MA0091.10.777
MA0092.10.799
MA0093.10.778
MA0099.21.21921e-23
MA0100.10.66
MA0101.10.00321
MA0102.20.418
MA0103.10.0302
MA0104.20.939
MA0105.10.261
MA0106.10.525
MA0107.10.00134
MA0108.20.026
MA0111.10.547
MA0112.20.349
MA0113.10.806
MA0114.10.977
MA0115.10.145
MA0116.10.992
MA0117.10.725
MA0119.10.405
MA0122.10.699
MA0124.10.86
MA0125.10.644
MA0131.10.674
MA0135.10.178
MA0136.11.75766e-7
MA0137.20.207
MA0138.20.339
MA0139.10.917
MA0140.10.872
MA0141.10.0401
MA0142.10.801
MA0143.10.539
MA0144.10.523
MA0145.10.306
MA0146.10.795
MA0147.10.847
MA0148.10.842
MA0149.10.0268
MA0150.10.00205
MA0152.10.104
MA0153.10.0424
MA0154.10.9
MA0155.10.937
MA0156.13.01825e-5
MA0157.10.859
MA0159.10.0849
MA0160.10.0241
MA0162.10.654
MA0163.10.0574
MA0164.10.196
MA0258.10.219
MA0259.10.084



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: CNhs13508

Novel motifP-value
10.419
100.798
1000.0228
1010.779
1020.778
1030.342
1040.501
1050.906
1060.246
1070.549
1080.615
1090.0382
110.632
1100.429
1110.315
1120.268
1130.163
1140.219
1150.81
1160.885
1170.665
1180.108
1190.411
120.301
1200.166
1210.825
1220.986
1230.0807
1240.547
1250.229
1260.705
1270.0612
1280.234
1290.452
130.0657
1300.792
1310.672
1320.492
1330.0123
1340.743
1350.516
1360.293
1370.861
1380.373
1390.717
140.525
1400.545
1410.861
1420.884
1430.023
1440.114
1450.884
1460.98
1470.169
1480.657
1490.597
150.0282
1500.212
1510.949
1520.0285
1530.671
1540.771
1550.537
1560.0565
1570.678
1580.835
1590.738
160.342
1600.956
1610.782
1620.387
1630.268
1640.983
1650.904
1660.327
1670.0899
1680.866
1690.8
170.994
180.11
190.589
20.254
200.16
210.609
220.74
230.143
240.0376
250.668
260.292
270.312
280.61
290.131
30.825
300.857
310.985
320.276
330.00224
340.0242
350.913
360.39
370.0214
380.578
390.2
40.0746
400.0109
410.955
420.808
430.122
440.0184
450.679
460.286
470.916
480.869
490.2
50.279
500.411
510.815
520.238
530.0208
540.948
550.667
560.723
570.974
580.73
590.793
60.843
600.142
610.783
620.935
630.911
640.47
650.249
661.82374e-4
670.542
680.301
690.413
70.305
700.173
710.378
720.706
730.0223
740.793
750.854
760.216
770.432
780.452
790.585
80.0316
800.871
810.64
820.56
830.0162
840.921
850.0848
860.844
870.00664
880.997
890.869
90.414
900.654
910.836
920.864
930.919
940.941
950.0585
960.591
970.509
980.661
990.706



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: CNhs13508


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)

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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