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FF:11759-123H4: 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, 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 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-penis0.0529
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-lymphoma0.0213
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: CNhs12375

Jaspar motifP-value
MA0002.20.887
MA0003.10.929
MA0004.10.9
MA0006.10.492
MA0007.10.367
MA0009.10.454
MA0014.10.597
MA0017.10.37
MA0018.20.0454
MA0019.10.483
MA0024.13.44312e-6
MA0025.10.381
MA0027.10.577
MA0028.10.152
MA0029.10.857
MA0030.10.266
MA0031.10.181
MA0035.20.0155
MA0038.10.0214
MA0039.20.00129
MA0040.10.559
MA0041.10.819
MA0042.10.667
MA0043.10.0391
MA0046.10.193
MA0047.20.755
MA0048.10.0921
MA0050.10.0159
MA0051.10.0688
MA0052.10.977
MA0055.10.512
MA0057.10.779
MA0058.10.961
MA0059.10.734
MA0060.12.05881e-9
MA0061.10.0346
MA0062.27.98147e-5
MA0065.20.0134
MA0066.10.562
MA0067.10.734
MA0068.10.0301
MA0069.10.921
MA0070.10.894
MA0071.10.64
MA0072.10.529
MA0073.10.836
MA0074.10.184
MA0076.10.0334
MA0077.10.442
MA0078.10.765
MA0079.20.0818
MA0080.23.06691e-4
MA0081.10.0265
MA0083.14.0093e-9
MA0084.10.0406
MA0087.10.739
MA0088.10.972
MA0090.10.00163
MA0091.10.267
MA0092.10.669
MA0093.10.672
MA0099.22.11963e-16
MA0100.10.699
MA0101.10.00882
MA0102.20.911
MA0103.13.6134e-5
MA0104.20.245
MA0105.10.00523
MA0106.10.175
MA0107.10.00452
MA0108.20.00117
MA0111.10.465
MA0112.20.0834
MA0113.10.396
MA0114.10.0292
MA0115.10.0416
MA0116.10.758
MA0117.10.38
MA0119.10.171
MA0122.10.601
MA0124.10.654
MA0125.10.0668
MA0131.10.768
MA0135.10.109
MA0136.12.24872e-4
MA0137.20.535
MA0138.20.699
MA0139.10.685
MA0140.10.115
MA0141.10.817
MA0142.10.297
MA0143.10.828
MA0144.10.598
MA0145.10.992
MA0146.10.183
MA0147.10.386
MA0148.10.818
MA0149.10.926
MA0150.10.00139
MA0152.10.00143
MA0153.10.606
MA0154.10.406
MA0155.10.416
MA0156.10.0131
MA0157.10.197
MA0159.10.45
MA0160.10.335
MA0162.10.142
MA0163.10.0691
MA0164.10.675
MA0258.10.815
MA0259.10.831



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: CNhs12375

Novel motifP-value
10.783
100.244
1000.259
1010.582
1020.253
1030.776
1040.947
1050.853
1060.151
1070.387
1080.904
1090.986
110.668
1100.0534
1110.316
1120.539
1130.00467
1140.464
1150.485
1160.344
1170.177
1180.719
1190.275
120.458
1200.0814
1210.876
1220.0619
1230.00372
1240.458
1250.99
1260.695
1270.984
1280.408
1290.573
130.446
1300.421
1310.0365
1320.758
1330.888
1340.12
1350.733
1360.481
1370.862
1380.557
1390.406
140.178
1400.356
1410.511
1420.622
1430.0352
1440.618
1450.546
1460.581
1470.0457
1480.799
1490.308
150.443
1500.0517
1510.487
1520.192
1530.825
1540.82
1550.00328
1560.285
1570.31
1580.038
1590.0929
160.0226
1600.317
1610.359
1620.614
1630.221
1640.0798
1650.928
1660.438
1670.942
1680.794
1690.455
170.286
180.0656
190.0928
20.596
200.809
210.891
220.716
230.0113
240.429
250.19
260.301
270.757
280.255
290.204
30.434
300.776
310.77
323.05195e-7
330.863
340.903
350.208
360.108
370.072
380.734
390.383
40.499
400.145
410.816
420.981
430.656
440.33
450.54
460.328
470.515
480.644
490.221
50.306
500.446
510.899
520.835
530.125
540.977
550.184
560.512
570.955
580.217
590.768
60.321
600.57
610.894
620.969
630.715
640.856
650.358
660.132
670.508
680.891
690.386
70.31
700.874
710.413
720.77
730.0801
740.0477
750.463
760.537
770.0243
780.255
790.0596
80.676
800.767
810.545
820.777
830.872
840.915
850.0367
860.201
870.311
880.714
890.214
90.308
900.675
910.924
920.528
930.938
940.666
950.464
960.481
970.0971
980.0992
990.327



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: CNhs12375


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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