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FF:11835-124G8: 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 17:29, 29 March 2012


Name:mesenchymal precursor cell - ovarian cancer metastasis, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueovary
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-penis0.153
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-0.284
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: CNhs13093

Jaspar motifP-value
MA0002.20.578
MA0003.10.494
MA0004.10.253
MA0006.10.0847
MA0007.10.627
MA0009.10.903
MA0014.10.511
MA0017.10.661
MA0018.22.03108e-4
MA0019.10.474
MA0024.13.22273e-8
MA0025.10.0207
MA0027.10.36
MA0028.11.5489e-4
MA0029.10.63
MA0030.10.0115
MA0031.10.00808
MA0035.20.0598
MA0038.10.00391
MA0039.20.0823
MA0040.10.844
MA0041.10.344
MA0042.10.477
MA0043.12.13607e-4
MA0046.10.0432
MA0047.20.111
MA0048.10.674
MA0050.10.0953
MA0051.10.335
MA0052.10.301
MA0055.10.699
MA0057.10.695
MA0058.10.0426
MA0059.10.724
MA0060.15.96023e-15
MA0061.10.768
MA0062.22.67195e-12
MA0065.20.437
MA0066.10.124
MA0067.10.00592
MA0068.10.775
MA0069.10.05
MA0070.10.429
MA0071.10.611
MA0072.10.21
MA0073.10.418
MA0074.10.224
MA0076.12.9253e-7
MA0077.10.856
MA0078.10.813
MA0079.20.0291
MA0080.22.13838e-8
MA0081.10.00203
MA0083.18.59233e-8
MA0084.10.81
MA0087.10.356
MA0088.10.216
MA0090.10.0123
MA0091.10.0251
MA0092.10.113
MA0093.10.279
MA0099.20.0762
MA0100.10.139
MA0101.10.744
MA0102.20.217
MA0103.10.0487
MA0104.20.00822
MA0105.10.251
MA0106.10.139
MA0107.10.837
MA0108.25.72201e-4
MA0111.10.855
MA0112.20.0048
MA0113.10.619
MA0114.10.636
MA0115.10.0774
MA0116.10.881
MA0117.10.21
MA0119.10.0955
MA0122.10.882
MA0124.10.257
MA0125.10.153
MA0131.10.129
MA0135.10.13
MA0136.15.00458e-12
MA0137.20.00173
MA0138.20.949
MA0139.10.776
MA0140.10.144
MA0141.10.306
MA0142.10.0857
MA0143.10.966
MA0144.10.576
MA0145.10.204
MA0146.10.79
MA0147.10.0325
MA0148.10.116
MA0149.10.761
MA0150.10.993
MA0152.10.0738
MA0153.10.27
MA0154.10.494
MA0155.10.133
MA0156.14.50367e-9
MA0157.10.115
MA0159.10.362
MA0160.10.123
MA0162.10.0248
MA0163.10.0637
MA0164.10.505
MA0258.10.123
MA0259.10.316



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: CNhs13093

Novel motifP-value
10.812
100.954
1000.846
1010.832
1020.536
1030.592
1040.823
1050.106
1069.29043e-4
1070.016
1080.0504
1090.779
110.68
1100.458
1110.849
1120.132
1130.809
1140.235
1150.203
1160.0898
1170.816
1180.852
1190.627
120.594
1200.176
1210.757
1220.00433
1230.423
1240.34
1250.274
1260.848
1270.574
1280.231
1290.291
130.51
1300.0606
1310.614
1320.376
1330.764
1340.542
1350.564
1360.645
1370.113
1380.475
1390.679
140.134
1400.283
1410.672
1420.397
1430.313
1440.501
1450.237
1460.445
1470.111
1480.683
1490.121
150.952
1500.227
1510.629
1520.0253
1530.233
1540.797
1550.136
1560.791
1570.87
1580.255
1590.874
160.122
1600.421
1610.667
1620.113
1630.155
1640.0719
1650.618
1660.0526
1670.653
1680.863
1690.0411
170.211
180.101
190.0441
20.36
200.363
210.128
220.553
230.0453
240.395
250.0271
260.48
270.476
280.163
290.43
30.6
300.66
310.813
328.55417e-11
330.83
340.763
350.604
360.0979
370.0493
380.441
390.186
40.76
400.675
410.632
420.243
430.817
440.491
450.973
460.226
470.879
480.71
490.98
50.74
500.435
510.892
520.601
530.302
540.671
550.128
560.867
570.43
580.387
590.298
60.551
600.595
610.619
620.939
630.291
640.615
650.631
660.0281
670.508
680.972
690.986
70.0645
700.0641
710.293
720.326
730.023
740.165
750.821
760.871
770.0633
780.859
791.89779e-4
80.218
800.48
810.743
820.522
830.197
840.617
850.0321
860.986
870.583
880.709
890.193
90.718
900.858
910.695
920.279
930.889
940.362
950.608
960.734
970.513
980.696
990.0129



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: CNhs13093


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)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
120 (female reproductive organ cancer)
14566 (disease of cellular proliferation)
162 (cancer)
193 (reproductive organ cancer)
2394 (ovarian cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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