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FF:11760-123H5: 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 17:19, 29 March 2012


Name:mesenchymal precursor cell - ovarian cancer left ovary, donor3
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 typeNA
extraction protocol (Details)NA
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-penis0.01
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-lymphoma0.0985
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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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: CNhs12376

Jaspar motifP-value
MA0002.20.165
MA0003.10.637
MA0004.10.0841
MA0006.10.379
MA0007.10.978
MA0009.10.185
MA0014.10.89
MA0017.10.101
MA0018.20.0182
MA0019.10.196
MA0024.10.143
MA0025.10.625
MA0027.10.673
MA0028.10.242
MA0029.10.564
MA0030.10.214
MA0031.10.108
MA0035.20.103
MA0038.10.394
MA0039.20.0347
MA0040.10.642
MA0041.10.515
MA0042.10.982
MA0043.10.234
MA0046.10.549
MA0047.20.721
MA0048.10.118
MA0050.10.118
MA0051.10.461
MA0052.10.05
MA0055.10.167
MA0057.10.97
MA0058.10.0182
MA0059.10.244
MA0060.10.0385
MA0061.10.665
MA0062.20.246
MA0065.20.00248
MA0066.10.129
MA0067.10.0175
MA0068.10.122
MA0069.10.612
MA0070.10.784
MA0071.10.104
MA0072.10.244
MA0073.10.926
MA0074.10.989
MA0076.10.34
MA0077.10.788
MA0078.10.814
MA0079.20.428
MA0080.27.50352e-8
MA0081.10.0348
MA0083.11.73577e-7
MA0084.10.153
MA0087.10.587
MA0088.10.421
MA0090.10.00274
MA0091.10.761
MA0092.10.952
MA0093.10.193
MA0099.23.67652e-9
MA0100.10.701
MA0101.10.166
MA0102.20.929
MA0103.15.12456e-4
MA0104.20.00328
MA0105.10.951
MA0106.10.235
MA0107.10.092
MA0108.23.2948e-5
MA0111.10.19
MA0112.20.103
MA0113.10.873
MA0114.10.0184
MA0115.10.0333
MA0116.10.0274
MA0117.10.729
MA0119.10.978
MA0122.10.214
MA0124.10.391
MA0125.10.254
MA0131.10.962
MA0135.10.143
MA0136.12.64004e-6
MA0137.20.982
MA0138.20.156
MA0139.10.313
MA0140.10.259
MA0141.10.031
MA0142.10.595
MA0143.10.717
MA0144.10.857
MA0145.10.828
MA0146.10.136
MA0147.10.0144
MA0148.10.926
MA0149.10.428
MA0150.10.282
MA0152.10.0041
MA0153.10.608
MA0154.10.209
MA0155.10.358
MA0156.10.0888
MA0157.10.106
MA0159.10.0753
MA0160.10.00936
MA0162.10.289
MA0163.10.117
MA0164.10.992
MA0258.10.014
MA0259.10.435



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: CNhs12376

Novel motifP-value
10.173
100.341
1000.443
1010.936
1020.142
1030.895
1040.773
1050.335
1060.959
1070.364
1080.674
1090.158
110.478
1100.52
1110.0621
1120.429
1130.0177
1140.327
1150.751
1160.511
1170.919
1180.307
1190.407
120.327
1200.214
1210.757
1220.0499
1238.68673e-4
1240.328
1250.798
1260.546
1270.877
1280.918
1290.647
130.23
1300.619
1310.072
1320.856
1330.706
1340.463
1350.826
1360.937
1370.876
1380.706
1390.748
140.169
1400.401
1410.569
1420.991
1430.63
1440.747
1450.712
1460.599
1470.235
1480.174
1490.497
150.492
1500.254
1510.157
1520.177
1530.505
1540.801
1550.00118
1560.264
1570.145
1580.00284
1590.135
160.314
1600.581
1610.353
1620.605
1630.488
1640.761
1650.981
1660.427
1670.209
1680.873
1690.625
170.734
180.619
190.936
20.743
200.609
210.331
220.767
230.347
240.808
250.0802
260.538
270.719
280.49
290.992
30.717
300.472
310.599
320.0019
330.935
340.926
350.668
360.0365
370.837
380.221
390.424
40.173
400.101
410.232
420.638
430.269
440.659
450.713
460.45
470.205
480.485
490.00693
50.74
500.796
510.476
520.984
530.105
540.591
550.287
560.517
570.302
580.0693
590.407
60.209
600.513
610.195
620.209
630.534
640.408
650.546
660.825
670.986
680.756
690.0649
70.0693
700.0889
710.389
720.405
730.584
740.1
750.803
760.658
770.625
780.0194
790.094
80.603
800.553
810.254
820.176
830.954
840.831
850.935
860.994
870.504
880.977
890.666
90.666
900.997
910.748
920.755
930.625
940.655
950.614
960.482
970.244
980.00673
990.0323



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: CNhs12376


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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