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FF:11756-123H1: 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 left 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-penis0.0379
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-lymphoma0.143
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: CNhs12372

Jaspar motifP-value
MA0002.20.518
MA0003.10.649
MA0004.10.0782
MA0006.10.47
MA0007.10.852
MA0009.10.206
MA0014.10.851
MA0017.10.197
MA0018.23.59752e-5
MA0019.10.327
MA0024.10.0459
MA0025.10.103
MA0027.10.923
MA0028.10.912
MA0029.10.32
MA0030.10.134
MA0031.10.198
MA0035.20.0714
MA0038.10.172
MA0039.20.0102
MA0040.10.658
MA0041.10.502
MA0042.10.837
MA0043.18.0101e-4
MA0046.10.0605
MA0047.20.565
MA0048.10.15
MA0050.10.0665
MA0051.10.501
MA0052.10.152
MA0055.10.401
MA0057.10.698
MA0058.10.0305
MA0059.10.579
MA0060.19.5868e-5
MA0061.10.431
MA0062.20.0208
MA0065.20.00242
MA0066.10.655
MA0067.10.0219
MA0068.10.276
MA0069.10.714
MA0070.10.994
MA0071.10.228
MA0072.10.361
MA0073.10.833
MA0074.10.355
MA0076.10.706
MA0077.10.945
MA0078.10.619
MA0079.20.153
MA0080.27.14071e-5
MA0081.10.0983
MA0083.15.77886e-4
MA0084.10.0871
MA0087.10.552
MA0088.10.732
MA0090.14.63187e-4
MA0091.10.786
MA0092.10.941
MA0093.10.232
MA0099.25.73956e-15
MA0100.10.643
MA0101.10.0818
MA0102.20.835
MA0103.11.80697e-4
MA0104.20.00647
MA0105.10.0914
MA0106.10.0749
MA0107.10.0586
MA0108.20.0089
MA0111.10.119
MA0112.20.973
MA0113.10.966
MA0114.10.0324
MA0115.10.19
MA0116.10.239
MA0117.10.84
MA0119.10.447
MA0122.10.717
MA0124.10.309
MA0125.10.384
MA0131.10.669
MA0135.10.129
MA0136.17.55281e-4
MA0137.20.91
MA0138.20.0721
MA0139.10.875
MA0140.10.335
MA0141.10.0675
MA0142.10.433
MA0143.10.618
MA0144.10.744
MA0145.10.813
MA0146.10.116
MA0147.10.0517
MA0148.10.806
MA0149.10.723
MA0150.10.0394
MA0152.10.00555
MA0153.10.277
MA0154.10.766
MA0155.10.659
MA0156.10.36
MA0157.10.337
MA0159.10.135
MA0160.10.0225
MA0162.10.0702
MA0163.10.701
MA0164.10.908
MA0258.10.118
MA0259.10.398



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: CNhs12372

Novel motifP-value
10.673
100.496
1000.317
1010.923
1020.193
1030.709
1040.992
1050.303
1060.884
1070.499
1080.734
1090.455
110.729
1100.184
1110.107
1120.914
1130.0087
1140.646
1150.448
1160.562
1170.842
1180.579
1190.666
120.336
1200.145
1210.772
1220.24
1231.95607e-4
1240.187
1250.973
1260.515
1270.574
1280.851
1290.862
130.439
1300.616
1310.0111
1320.803
1330.659
1340.471
1350.487
1360.969
1370.958
1380.618
1390.667
140.0895
1400.98
1410.595
1420.428
1430.123
1440.922
1450.679
1460.555
1470.0294
1480.658
1490.594
150.816
1500.141
1510.402
1520.32
1530.978
1540.633
1552.0594e-4
1560.468
1570.249
1580.00923
1590.122
160.0962
1600.904
1610.213
1620.783
1630.111
1640.45
1650.936
1660.187
1670.313
1680.985
1690.867
170.867
180.114
190.626
20.484
200.55
210.656
220.875
230.0813
240.225
250.126
260.925
270.951
280.521
290.622
30.923
300.518
310.585
320.00176
330.795
340.699
350.932
360.0404
370.318
380.434
390.127
40.196
400.0635
410.945
420.814
430.586
440.868
450.808
460.952
470.243
480.799
490.0149
50.963
500.674
510.772
520.789
530.0251
540.879
550.283
560.533
570.686
580.123
590.649
60.499
600.544
610.425
620.428
630.916
640.517
650.739
660.662
670.559
680.683
690.133
70.137
700.254
710.374
720.638
730.16
740.569
750.709
760.933
770.323
780.0832
790.04
80.812
800.921
810.778
820.344
830.758
840.583
850.762
860.873
870.354
880.945
890.341
90.494
900.409
910.964
920.928
930.878
940.89
950.534
960.956
970.264
980.00911
990.0292



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: CNhs12372


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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