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FF:11838-124H2: 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 metastasis, 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-penis0.365
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-0.235
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs13097

Jaspar motifP-value
MA0002.20.479
MA0003.10.764
MA0004.10.0214
MA0006.10.0397
MA0007.10.285
MA0009.10.711
MA0014.10.917
MA0017.10.049
MA0018.21.70224e-6
MA0019.10.914
MA0024.16.87284e-9
MA0025.10.00662
MA0027.10.412
MA0028.10.00154
MA0029.10.588
MA0030.10.125
MA0031.10.00328
MA0035.20.48
MA0038.12.49168e-5
MA0039.20.256
MA0040.10.861
MA0041.10.906
MA0042.10.827
MA0043.18.8553e-5
MA0046.10.00537
MA0047.20.00631
MA0048.10.296
MA0050.10.0487
MA0051.10.965
MA0052.10.00756
MA0055.10.586
MA0057.10.251
MA0058.10.00792
MA0059.10.821
MA0060.12.73418e-16
MA0061.10.953
MA0062.21.73183e-8
MA0065.20.469
MA0066.10.131
MA0067.10.00763
MA0068.10.11
MA0069.10.195
MA0070.10.908
MA0071.10.827
MA0072.10.441
MA0073.10.918
MA0074.10.306
MA0076.11.37574e-5
MA0077.10.645
MA0078.10.989
MA0079.20.709
MA0080.22.9323e-9
MA0081.10.00399
MA0083.10.0117
MA0084.10.861
MA0087.10.439
MA0088.10.221
MA0090.12.16704e-4
MA0091.10.646
MA0092.10.0892
MA0093.10.0275
MA0099.20.00324
MA0100.10.018
MA0101.10.116
MA0102.20.246
MA0103.10.358
MA0104.20.0107
MA0105.10.447
MA0106.10.0643
MA0107.10.317
MA0108.20.346
MA0111.10.32
MA0112.20.0138
MA0113.10.855
MA0114.10.234
MA0115.10.247
MA0116.10.932
MA0117.10.582
MA0119.10.0412
MA0122.10.852
MA0124.10.0661
MA0125.10.156
MA0131.10.395
MA0135.10.0218
MA0136.15.10816e-12
MA0137.20.0489
MA0138.20.551
MA0139.10.792
MA0140.10.277
MA0141.10.473
MA0142.10.128
MA0143.10.831
MA0144.10.612
MA0145.10.19
MA0146.10.736
MA0147.10.0334
MA0148.10.135
MA0149.10.47
MA0150.10.59
MA0152.10.0799
MA0153.10.36
MA0154.10.943
MA0155.10.209
MA0156.12.7783e-7
MA0157.10.101
MA0159.10.198
MA0160.10.106
MA0162.10.0236
MA0163.10.0603
MA0164.10.215
MA0258.10.425
MA0259.10.246



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: CNhs13097

Novel motifP-value
10.867
100.461
1000.73
1010.863
1020.523
1030.598
1040.549
1050.0785
1060.0168
1070.0371
1080.0854
1090.867
110.369
1100.364
1110.437
1120.253
1130.043
1140.0558
1150.0175
1160.159
1170.38
1180.199
1190.827
120.383
1200.197
1210.909
1220.455
1230.0868
1240.337
1250.479
1260.694
1270.949
1280.0996
1290.991
130.641
1300.108
1310.0855
1320.294
1330.944
1340.997
1350.189
1360.761
1370.149
1380.505
1390.259
140.393
1400.47
1410.613
1420.543
1430.919
1440.205
1450.409
1460.301
1470.0843
1480.525
1490.0655
150.521
1500.207
1510.537
1520.0142
1530.864
1540.662
1550.187
1560.741
1570.886
1580.134
1590.88
160.0181
1600.457
1610.998
1620.367
1630.0138
1640.0162
1650.528
1660.315
1670.939
1680.166
1690.0743
170.273
180.533
190.255
20.493
200.642
210.487
220.463
230.0866
240.835
250.0373
260.657
270.593
280.787
290.307
30.287
300.851
310.795
329.04696e-9
330.889
340.856
350.888
360.0261
370.0186
380.585
390.131
40.235
400.737
410.349
420.41
430.443
440.217
450.979
460.512
470.997
480.796
490.801
50.848
500.937
510.777
520.587
530.114
540.453
550.203
560.848
570.424
580.283
590.365
60.953
600.682
610.287
620.512
630.233
640.639
650.813
660.14
670.476
680.949
690.325
70.135
700.0638
710.32
720.835
730.0122
740.13
750.683
760.443
770.0175
780.619
790.0145
80.0508
800.174
810.425
820.607
830.236
840.764
850.0816
860.777
870.188
880.541
890.0286
90.731
900.432
910.475
920.171
930.892
940.904
950.972
960.744
970.457
980.32
990.0727



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: CNhs13097


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)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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