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FF:11836-124G9: 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 left ovary, donor4
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-penis0.1
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-lymphoma0.0535
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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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: CNhs13094

Jaspar motifP-value
MA0002.20.668
MA0003.10.905
MA0004.10.127
MA0006.10.95
MA0007.10.378
MA0009.10.759
MA0014.10.401
MA0017.10.709
MA0018.21.24264e-5
MA0019.10.227
MA0024.19.85074e-4
MA0025.16.26562e-4
MA0027.10.299
MA0028.10.017
MA0029.10.882
MA0030.10.00176
MA0031.10.0606
MA0035.20.0143
MA0038.13.56012e-4
MA0039.20.0353
MA0040.10.766
MA0041.10.811
MA0042.10.839
MA0043.11.80647e-6
MA0046.10.111
MA0047.20.798
MA0048.10.482
MA0050.10.139
MA0051.10.071
MA0052.10.0918
MA0055.10.652
MA0057.10.498
MA0058.10.0659
MA0059.10.826
MA0060.12.75066e-15
MA0061.10.954
MA0062.21.51486e-7
MA0065.20.775
MA0066.10.641
MA0067.10.0338
MA0068.10.0221
MA0069.10.425
MA0070.10.596
MA0071.10.632
MA0072.10.0997
MA0073.10.92
MA0074.10.16
MA0076.16.72387e-4
MA0077.10.197
MA0078.10.63
MA0079.20.126
MA0080.22.8403e-7
MA0081.10.00338
MA0083.10.0297
MA0084.10.0504
MA0087.10.976
MA0088.10.826
MA0090.10.0097
MA0091.10.111
MA0092.10.381
MA0093.10.152
MA0099.28.05117e-4
MA0100.10.463
MA0101.10.0333
MA0102.20.137
MA0103.10.00859
MA0104.20.335
MA0105.10.00102
MA0106.10.135
MA0107.10.0201
MA0108.20.431
MA0111.10.475
MA0112.20.00216
MA0113.10.647
MA0114.10.712
MA0115.10.187
MA0116.13.38522e-4
MA0117.10.705
MA0119.10.00729
MA0122.10.253
MA0124.10.136
MA0125.10.202
MA0131.10.505
MA0135.10.224
MA0136.16.49593e-9
MA0137.20.96
MA0138.20.863
MA0139.10.655
MA0140.10.229
MA0141.10.528
MA0142.10.112
MA0143.10.81
MA0144.10.357
MA0145.10.657
MA0146.10.356
MA0147.10.872
MA0148.10.675
MA0149.10.736
MA0150.10.179
MA0152.10.0282
MA0153.10.867
MA0154.10.0617
MA0155.10.831
MA0156.11.86458e-5
MA0157.10.244
MA0159.10.615
MA0160.10.106
MA0162.10.347
MA0163.11.73058e-6
MA0164.10.663
MA0258.10.409
MA0259.10.659



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: CNhs13094

Novel motifP-value
10.186
100.105
1000.486
1010.688
1020.487
1030.193
1040.937
1050.0056
1060.0666
1070.0332
1080.61
1090.842
110.14
1100.0643
1110.628
1120.463
1130.182
1140.0144
1150.0308
1160.0748
1170.26
1180.875
1190.738
120.201
1200.166
1210.915
1220.0377
1230.102
1240.956
1250.448
1260.725
1270.871
1280.312
1290.236
130.966
1300.937
1310.351
1320.868
1330.418
1340.471
1350.667
1360.296
1370.86
1380.899
1390.457
140.123
1400.477
1410.663
1420.37
1430.554
1440.228
1450.144
1460.615
1470.138
1480.0147
1490.353
150.29
1500.216
1510.714
1520.431
1530.524
1540.717
1550.0891
1560.338
1570.844
1580.0678
1590.108
160.0246
1600.124
1610.495
1620.466
1630.241
1640.0583
1650.374
1660.00371
1670.97
1680.403
1690.0772
170.289
180.0942
190.0611
20.476
200.416
210.286
220.507
230.0223
240.761
250.189
260.118
270.485
280.232
290.0912
30.109
300.937
310.561
321.40416e-7
330.7
340.79
350.293
360.254
370.027
380.694
390.0944
40.248
400.495
410.641
420.412
430.23
440.348
450.627
460.0283
470.488
480.33
490.917
50.564
500.526
510.593
520.998
530.208
540.367
550.271
560.8
570.459
580.969
590.0775
60.187
600.62
610.678
620.33
630.161
640.958
650.266
660.295
670.653
680.626
690.748
70.462
700.115
710.0421
720.419
730.311
740.291
750.459
760.777
770.0444
780.693
790.0342
80.0187
800.473
810.178
820.256
830.637
840.687
850.137
860.253
870.965
880.565
890.0691
90.385
900.114
910.14
920.203
930.909
940.661
950.837
960.689
970.422
980.243
990.0288



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: CNhs13094


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)
0000062 (organ)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial 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)
0000991 (gonad)
0000992 (female gonad)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002119 (left ovary)
0002323 (body cavity)
0002384 (connective tissue)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0004120 (mesoderm-derived structure)
0004176 (external genitalia)
0004458 (body cavity or lining)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005564 (gonad primordium)
0009117 (indifferent gonad)
0009196 (indifferent external genitalia)

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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