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FF:11837-124H1: 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 right 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-penis0.203
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-lymphoma-0.155
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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: CNhs13096

Jaspar motifP-value
MA0002.20.171
MA0003.10.988
MA0004.10.0249
MA0006.10.131
MA0007.10.462
MA0009.10.663
MA0014.10.145
MA0017.10.058
MA0018.23.48088e-5
MA0019.10.767
MA0024.12.28418e-7
MA0025.19.82252e-4
MA0027.10.666
MA0028.18.37702e-5
MA0029.10.94
MA0030.10.0226
MA0031.10.00941
MA0035.20.004
MA0038.16.83702e-4
MA0039.20.00104
MA0040.10.921
MA0041.10.385
MA0042.10.398
MA0043.13.95722e-4
MA0046.10.19
MA0047.20.237
MA0048.10.249
MA0050.10.334
MA0051.10.727
MA0052.10.184
MA0055.10.174
MA0057.10.348
MA0058.10.00162
MA0059.10.463
MA0060.17.08641e-18
MA0061.10.654
MA0062.21.23831e-12
MA0065.20.118
MA0066.10.625
MA0067.10.0116
MA0068.10.887
MA0069.10.176
MA0070.10.796
MA0071.10.996
MA0072.10.447
MA0073.10.581
MA0074.10.387
MA0076.12.5374e-6
MA0077.10.944
MA0078.10.598
MA0079.20.0672
MA0080.22.39888e-8
MA0081.10.00277
MA0083.14.81742e-7
MA0084.10.232
MA0087.10.557
MA0088.10.224
MA0090.10.00441
MA0091.10.142
MA0092.10.307
MA0093.10.0193
MA0099.20.513
MA0100.10.0462
MA0101.10.256
MA0102.20.293
MA0103.10.0113
MA0104.20.00109
MA0105.10.892
MA0106.10.00619
MA0107.10.35
MA0108.20.024
MA0111.10.562
MA0112.20.0219
MA0113.10.72
MA0114.10.124
MA0115.10.0524
MA0116.10.613
MA0117.10.274
MA0119.10.0386
MA0122.10.552
MA0124.10.297
MA0125.10.257
MA0131.10.169
MA0135.10.0901
MA0136.18.89346e-11
MA0137.20.0101
MA0138.20.888
MA0139.10.807
MA0140.10.0207
MA0141.10.312
MA0142.10.205
MA0143.10.692
MA0144.10.634
MA0145.10.647
MA0146.10.376
MA0147.10.0286
MA0148.10.408
MA0149.10.65
MA0150.10.407
MA0152.10.0754
MA0153.10.18
MA0154.10.949
MA0155.10.321
MA0156.17.54596e-9
MA0157.10.0733
MA0159.10.859
MA0160.10.0689
MA0162.10.0273
MA0163.10.0325
MA0164.10.49
MA0258.10.455
MA0259.10.234



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: CNhs13096

Novel motifP-value
10.63
100.894
1000.826
1010.849
1020.42
1030.944
1040.969
1050.0314
1060.00388
1070.0211
1080.11
1090.536
110.731
1100.277
1110.741
1120.216
1130.423
1140.136
1150.0811
1160.112
1170.882
1180.816
1190.69
120.28
1200.0938
1210.668
1220.0196
1230.355
1240.198
1250.821
1260.987
1270.454
1280.225
1290.603
130.443
1300.304
1310.42
1320.319
1330.591
1340.868
1350.455
1360.928
1370.244
1380.72
1390.23
140.179
1400.429
1410.71
1420.979
1430.766
1440.264
1450.246
1460.509
1470.05
1480.835
1490.0737
150.972
1500.119
1510.534
1520.0318
1530.775
1540.781
1550.0707
1560.868
1570.786
1580.315
1590.877
160.0866
1600.723
1610.911
1620.182
1630.121
1640.017
1650.693
1660.0873
1670.439
1680.492
1690.202
170.309
180.248
190.0264
20.422
200.579
210.182
220.856
230.109
240.568
250.0417
260.799
270.698
280.283
290.698
30.505
300.915
310.899
321.08368e-8
330.567
340.936
350.601
360.0573
370.0902
380.503
390.217
40.355
400.549
410.835
420.46
430.912
440.543
450.556
460.294
470.441
480.748
490.743
50.713
500.403
510.922
520.886
530.236
540.808
550.36
560.967
570.545
580.181
590.601
60.532
600.974
610.406
620.781
630.312
640.347
650.719
660.0386
670.387
680.629
690.536
70.0634
700.112
710.435
720.611
730.0173
740.14
750.941
760.821
770.12
780.777
798.02402e-4
80.159
800.141
810.905
820.894
830.407
840.645
850.0441
860.827
870.695
880.651
890.568
90.951
900.853
910.331
920.413
930.781
940.615
950.75
960.663
970.516
980.32
990.0406



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: CNhs13096


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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