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FF:11833-124G6: 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 left 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 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-penis0.0532
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-0.444
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: CNhs13092

Jaspar motifP-value
MA0002.20.329
MA0003.10.837
MA0004.10.0574
MA0006.10.551
MA0007.10.606
MA0009.10.467
MA0014.10.872
MA0017.10.821
MA0018.23.01699e-4
MA0019.10.0242
MA0024.12.4081e-10
MA0025.10.00351
MA0027.10.618
MA0028.10.0209
MA0029.10.51
MA0030.10.441
MA0031.10.687
MA0035.20.00525
MA0038.10.0055
MA0039.20.0182
MA0040.10.628
MA0041.10.959
MA0042.10.759
MA0043.10.0905
MA0046.10.0178
MA0047.20.978
MA0048.10.18
MA0050.17.19239e-4
MA0051.10.00391
MA0052.10.0208
MA0055.10.756
MA0057.10.686
MA0058.10.0725
MA0059.10.285
MA0060.19.31174e-13
MA0061.10.00358
MA0062.20.594
MA0065.20.719
MA0066.10.611
MA0067.10.429
MA0068.10.841
MA0069.10.283
MA0070.10.881
MA0071.10.89
MA0072.10.705
MA0073.10.561
MA0074.10.972
MA0076.10.449
MA0077.10.794
MA0078.11
MA0079.20.199
MA0080.24.25552e-6
MA0081.10.0292
MA0083.10.7
MA0084.10.0252
MA0087.10.237
MA0088.10.547
MA0090.10.277
MA0091.10.863
MA0092.10.632
MA0093.10.0294
MA0099.28.14316e-6
MA0100.10.181
MA0101.10.00157
MA0102.20.284
MA0103.10.00509
MA0104.20.748
MA0105.10.00861
MA0106.10.0293
MA0107.15.20964e-4
MA0108.20.65
MA0111.10.412
MA0112.20.202
MA0113.10.169
MA0114.10.987
MA0115.10.09
MA0116.10.533
MA0117.10.337
MA0119.10.334
MA0122.10.385
MA0124.10.818
MA0125.10.298
MA0131.10.381
MA0135.10.196
MA0136.15.83039e-4
MA0137.20.698
MA0138.20.426
MA0139.10.433
MA0140.10.0193
MA0141.10.787
MA0142.10.0114
MA0143.10.464
MA0144.10.431
MA0145.10.363
MA0146.10.727
MA0147.10.914
MA0148.10.75
MA0149.10.978
MA0150.10.0167
MA0152.10.0144
MA0153.10.527
MA0154.10.862
MA0155.10.705
MA0156.10.106
MA0157.10.251
MA0159.10.353
MA0160.10.657
MA0162.10.0676
MA0163.10.00403
MA0164.10.173
MA0258.10.594
MA0259.10.567



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: CNhs13092

Novel motifP-value
10.761
100.0769
1000.153
1010.446
1020.227
1030.63
1040.528
1050.0264
1060.0415
1070.276
1080.452
1090.346
110.743
1100.552
1110.168
1120.726
1130.502
1140.0659
1150.758
1160.139
1170.0594
1180.326
1190.773
120.752
1200.295
1210.507
1220.0175
1230.651
1240.0729
1250.851
1260.697
1270.45
1280.583
1290.988
130.359
1300.301
1310.224
1320.775
1330.825
1340.964
1350.827
1360.909
1370.805
1380.231
1390.29
140.333
1400.559
1410.667
1420.361
1430.285
1440.202
1450.174
1460.204
1470.566
1480.525
1490.393
150.214
1500.146
1510.754
1520.144
1530.648
1540.83
1550.03
1560.13
1570.25
1580.445
1590.786
160.154
1600.68
1610.22
1620.607
1630.682
1644.71072e-4
1650.74
1660.22
1670.0476
1680.2
1690.356
170.923
180.0339
190.359
20.89
200.386
210.0858
220.554
230.381
240.995
250.0149
260.519
270.908
280.724
290.103
30.669
300.149
310.792
324.21802e-5
330.968
340.644
350.195
360.441
370.00439
380.257
390.464
40.0659
400.417
410.269
420.138
430.533
440.928
450.747
460.699
470.424
480.905
490.302
50.672
500.335
510.466
520.912
530.347
540.892
550.0672
560.881
570.886
580.143
590.37
60.0925
600.671
610.639
620.111
630.227
640.68
650.58
660.0425
670.499
680.906
690.203
70.0993
700.261
710.0799
720.613
730.0135
740.00267
750.159
760.0285
770.213
780.0895
790.0423
80.854
800.0368
810.774
820.407
830.221
840.502
850.0937
860.632
870.519
880.924
890.489
90.694
900.104
910.585
920.175
930.815
940.83
950.824
960.141
970.29
980.105
990.433



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: CNhs13092


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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