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FF:11762-123H7: 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 17:19, 29 March 2012


Name:mesenchymal precursor cell - ovarian cancer metastasis, donor3
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
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-0.198
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: CNhs12378

Jaspar motifP-value
MA0002.20.816
MA0003.10.406
MA0004.10.135
MA0006.10.102
MA0007.10.241
MA0009.10.367
MA0014.10.967
MA0017.10.517
MA0018.20.0144
MA0019.10.138
MA0024.13.26936e-7
MA0025.10.18
MA0027.10.637
MA0028.10.0503
MA0029.10.697
MA0030.10.371
MA0031.10.13
MA0035.20.987
MA0038.10.05
MA0039.20.892
MA0040.10.38
MA0041.10.468
MA0042.10.54
MA0043.10.379
MA0046.10.335
MA0047.20.25
MA0048.10.149
MA0050.10.0174
MA0051.10.366
MA0052.10.0982
MA0055.10.124
MA0057.10.489
MA0058.10.161
MA0059.10.593
MA0060.19.57484e-9
MA0061.10.0786
MA0062.25.94609e-6
MA0065.20.797
MA0066.10.807
MA0067.10.162
MA0068.10.697
MA0069.10.378
MA0070.10.194
MA0071.10.986
MA0072.10.821
MA0073.10.935
MA0074.10.259
MA0076.10.00655
MA0077.10.183
MA0078.10.922
MA0079.20.8
MA0080.21.42119e-8
MA0081.19.10708e-5
MA0083.15.94541e-6
MA0084.10.871
MA0087.10.564
MA0088.10.198
MA0090.10.0014
MA0091.10.871
MA0092.10.22
MA0093.10.304
MA0099.23.68853e-7
MA0100.10.0607
MA0101.10.217
MA0102.20.9
MA0103.10.035
MA0104.20.044
MA0105.10.369
MA0106.10.188
MA0107.10.0177
MA0108.20.00646
MA0111.10.11
MA0112.20.0382
MA0113.10.652
MA0114.10.716
MA0115.10.212
MA0116.10.85
MA0117.10.854
MA0119.10.424
MA0122.10.569
MA0124.10.00782
MA0125.10.129
MA0131.10.105
MA0135.10.0531
MA0136.11.78917e-11
MA0137.20.885
MA0138.20.543
MA0139.10.696
MA0140.10.627
MA0141.10.43
MA0142.10.105
MA0143.10.967
MA0144.10.804
MA0145.10.161
MA0146.10.47
MA0147.10.0414
MA0148.10.648
MA0149.10.651
MA0150.10.0698
MA0152.10.03
MA0153.10.725
MA0154.10.417
MA0155.10.0476
MA0156.11.08428e-5
MA0157.10.142
MA0159.10.987
MA0160.10.23
MA0162.10.107
MA0163.10.622
MA0164.10.547
MA0258.10.331
MA0259.10.0814



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: CNhs12378

Novel motifP-value
10.929
100.442
1000.922
1010.958
1020.167
1030.275
1040.943
1050.664
1060.13
1070.0756
1080.588
1090.777
110.613
1100.127
1110.0262
1120.828
1130.0212
1140.735
1150.0846
1160.34
1170.867
1180.264
1190.995
120.543
1200.531
1210.867
1220.289
1231.12643e-4
1240.173
1250.301
1260.868
1270.746
1280.0506
1290.534
130.569
1300.829
1310.0517
1320.446
1330.309
1340.971
1350.505
1360.923
1370.612
1380.951
1390.186
140.264
1400.21
1410.402
1420.317
1430.585
1440.271
1450.951
1460.814
1470.0827
1480.257
1490.0459
150.685
1500.189
1510.839
1520.0529
1530.703
1540.934
1550.134
1560.611
1570.657
1580.0176
1590.317
160.0203
1600.836
1610.792
1620.423
1630.02
1640.0261
1650.689
1660.162
1670.161
1680.684
1690.0718
170.537
180.454
190.312
20.152
200.47
210.974
220.2
230.0113
240.869
250.0462
260.492
270.806
280.758
290.208
30.462
300.286
310.568
329.42625e-16
330.692
340.305
350.643
360.0944
370.191
380.454
390.329
40.549
400.963
410.4
420.354
430.325
440.436
450.426
460.721
470.553
480.97
490.474
50.956
500.789
510.523
520.353
530.053
540.491
550.521
560.702
570.863
580.283
590.164
60.647
600.522
610.623
620.766
630.579
640.996
650.452
660.322
670.874
680.842
690.645
70.294
700.331
710.515
720.917
730.146
740.00927
750.637
760.575
770.00915
780.683
790.00352
80.313
800.443
810.713
820.421
830.565
840.654
850.0325
860.949
870.274
880.635
890.152
90.341
900.244
910.882
920.0401
930.971
940.929
950.91
960.916
970.105
980.0113
990.0659



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: CNhs12378


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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