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FF:11757-123H2: 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 17:18, 29 March 2012


Name:mesenchymal precursor cell - ovarian cancer right ovary, donor1
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-penis0.0269
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-lymphoma0.463
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: CNhs12373

Jaspar motifP-value
MA0002.20.961
MA0003.10.914
MA0004.10.0027
MA0006.10.856
MA0007.10.54
MA0009.10.65
MA0014.10.67
MA0017.10.346
MA0018.25.11963e-5
MA0019.10.138
MA0024.10.614
MA0025.10.203
MA0027.10.974
MA0028.10.134
MA0029.10.633
MA0030.10.00954
MA0031.10.0105
MA0035.20.235
MA0038.10.748
MA0039.20.608
MA0040.10.956
MA0041.10.493
MA0042.10.692
MA0043.10.00314
MA0046.10.00618
MA0047.20.11
MA0048.10.302
MA0050.10.155
MA0051.10.756
MA0052.10.0428
MA0055.10.368
MA0057.10.492
MA0058.10.00248
MA0059.10.811
MA0060.10.00387
MA0061.10.41
MA0062.20.746
MA0065.20.217
MA0066.10.939
MA0067.10.0133
MA0068.10.146
MA0069.10.468
MA0070.10.856
MA0071.10.148
MA0072.10.297
MA0073.10.481
MA0074.10.635
MA0076.10.0621
MA0077.10.217
MA0078.10.875
MA0079.20.0262
MA0080.24.58273e-5
MA0081.10.0215
MA0083.10.00792
MA0084.10.818
MA0087.10.722
MA0088.10.723
MA0090.10.00595
MA0091.10.838
MA0092.10.118
MA0093.10.0172
MA0099.21.69386e-13
MA0100.10.507
MA0101.10.623
MA0102.20.352
MA0103.15.83655e-5
MA0104.20.215
MA0105.10.00156
MA0106.10.127
MA0107.10.802
MA0108.20.0461
MA0111.10.748
MA0112.20.0486
MA0113.10.891
MA0114.10.437
MA0115.10.658
MA0116.10.034
MA0117.10.965
MA0119.10.0337
MA0122.10.665
MA0124.10.273
MA0125.10.638
MA0131.10.447
MA0135.10.244
MA0136.10.00374
MA0137.20.12
MA0138.20.233
MA0139.10.178
MA0140.10.554
MA0141.10.0481
MA0142.10.82
MA0143.10.736
MA0144.10.202
MA0145.10.245
MA0146.10.184
MA0147.10.956
MA0148.10.404
MA0149.10.796
MA0150.10.086
MA0152.10.0744
MA0153.10.0953
MA0154.10.333
MA0155.10.835
MA0156.10.319
MA0157.10.217
MA0159.10.706
MA0160.10.0113
MA0162.10.0528
MA0163.10.00362
MA0164.10.917
MA0258.10.435
MA0259.10.621



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: CNhs12373

Novel motifP-value
10.323
100.335
1000.426
1010.727
1020.336
1030.162
1040.882
1050.147
1060.635
1070.293
1080.339
1090.831
110.866
1100.00812
1110.141
1120.807
1130.0318
1140.309
1150.612
1160.662
1170.285
1180.993
1190.483
120.41
1200.157
1210.884
1220.352
1235.9201e-4
1240.525
1250.574
1260.748
1270.777
1280.723
1290.793
130.162
1300.8
1310.00772
1320.825
1330.856
1340.922
1350.658
1360.706
1370.601
1380.857
1390.282
140.109
1400.698
1410.852
1420.732
1430.442
1440.826
1450.949
1460.981
1470.0382
1480.733
1490.398
150.313
1500.645
1510.501
1520.926
1530.835
1540.491
1550.00561
1560.356
1570.147
1580.0151
1590.128
160.103
1600.771
1610.33
1620.617
1630.0326
1640.497
1650.779
1660.412
1670.935
1680.792
1690.367
170.774
180.261
190.522
20.618
200.304
210.922
220.995
230.118
240.314
250.853
260.905
270.506
280.999
290.039
30.482
300.563
310.273
320.101
330.151
340.36
350.66
360.83
370.158
380.587
390.488
40.0741
400.979
410.902
420.786
430.737
440.99
450.408
460.526
470.979
480.801
490.0977
50.521
500.994
510.657
520.546
530.0404
540.385
550.128
560.46
570.938
580.884
590.94
60.249
600.681
610.558
620.55
630.753
640.468
650.449
660.905
670.55
680.851
690.466
70.844
700.245
710.0847
720.872
730.717
740.13
750.247
760.942
770.213
780.448
790.359
80.357
800.452
810.876
820.314
830.167
840.827
850.731
860.894
870.376
880.644
890.0732
90.484
900.192
910.964
920.671
930.529
940.781
950.243
960.504
970.244
980.134
990.0821



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: CNhs12373


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)
0002118 (right 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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