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FF:11758-123H3: 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 metastasis, 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-penis0.0579
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-0.151
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs12374

Jaspar motifP-value
MA0002.20.613
MA0003.10.675
MA0004.10.0856
MA0006.10.162
MA0007.10.647
MA0009.10.362
MA0014.10.946
MA0017.10.62
MA0018.22.80736e-6
MA0019.10.477
MA0024.11.47861e-6
MA0025.10.00452
MA0027.10.369
MA0028.10.304
MA0029.10.435
MA0030.10.00862
MA0031.10.0421
MA0035.20.0741
MA0038.10.00466
MA0039.20.0826
MA0040.10.593
MA0041.10.846
MA0042.10.754
MA0043.14.66775e-6
MA0046.10.0863
MA0047.20.528
MA0048.10.107
MA0050.10.0268
MA0051.10.28
MA0052.10.0261
MA0055.10.366
MA0057.10.0923
MA0058.10.0346
MA0059.10.842
MA0060.11.19159e-11
MA0061.10.793
MA0062.22.80341e-4
MA0065.20.168
MA0066.10.307
MA0067.10.0104
MA0068.10.0653
MA0069.10.346
MA0070.10.46
MA0071.10.719
MA0072.10.567
MA0073.10.831
MA0074.10.403
MA0076.10.134
MA0077.10.229
MA0078.10.706
MA0079.20.347
MA0080.22.74906e-7
MA0081.10.0116
MA0083.10.00182
MA0084.10.978
MA0087.10.681
MA0088.10.86
MA0090.10.00462
MA0091.10.226
MA0092.10.217
MA0093.10.14
MA0099.26.69172e-5
MA0100.10.478
MA0101.10.19
MA0102.20.0125
MA0103.10.0568
MA0104.20.0318
MA0105.10.204
MA0106.10.023
MA0107.10.431
MA0108.20.468
MA0111.10.382
MA0112.20.0121
MA0113.10.466
MA0114.10.3
MA0115.10.118
MA0116.10.303
MA0117.10.931
MA0119.10.029
MA0122.10.317
MA0124.10.106
MA0125.10.0197
MA0131.10.305
MA0135.10.0894
MA0136.11.81859e-7
MA0137.20.594
MA0138.20.989
MA0139.10.283
MA0140.10.4
MA0141.10.65
MA0142.10.207
MA0143.10.945
MA0144.10.68
MA0145.10.48
MA0146.10.555
MA0147.10.184
MA0148.10.849
MA0149.10.4
MA0150.10.329
MA0152.10.0967
MA0153.10.624
MA0154.10.338
MA0155.10.273
MA0156.18.40111e-4
MA0157.10.256
MA0159.10.961
MA0160.10.149
MA0162.10.0821
MA0163.10.0237
MA0164.10.666
MA0258.10.412
MA0259.10.55



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: CNhs12374

Novel motifP-value
10.421
100.712
1000.527
1010.761
1020.494
1030.206
1040.972
1050.281
1060.0697
1070.0294
1080.288
1090.384
110.238
1100.103
1110.8
1120.33
1130.0211
1140.0865
1150.134
1160.11
1170.509
1180.852
1190.472
120.285
1200.15
1210.749
1220.0936
1230.00198
1240.674
1250.655
1260.811
1270.296
1280.0737
1290.852
130.959
1300.386
1310.135
1320.398
1330.45
1340.343
1350.947
1360.623
1370.607
1380.763
1390.278
140.203
1400.657
1410.263
1420.612
1430.0874
1440.541
1450.485
1460.814
1470.0605
1480.534
1490.174
150.486
1500.134
1510.767
1520.0547
1530.367
1540.977
1550.0279
1560.511
1570.572
1580.0407
1590.159
160.0211
1600.494
1610.49
1620.572
1630.231
1640.0823
1650.88
1660.0646
1670.864
1680.683
1690.121
170.168
180.092
190.0629
20.649
200.586
210.469
220.357
230.0208
240.952
250.256
260.455
270.467
280.404
290.0935
30.299
300.629
310.561
325.50552e-10
330.76
340.85
350.441
360.0496
370.026
380.614
390.21
40.792
400.339
410.88
420.872
430.203
440.197
450.907
460.182
470.754
480.542
490.994
50.555
500.831
510.974
520.927
530.0596
540.811
550.112
560.928
570.914
580.519
590.178
60.536
600.701
610.689
620.576
630.424
640.73
650.439
660.29
670.293
680.995
690.47
70.226
700.171
710.383
720.906
730.0215
740.0991
750.362
760.593
770.0673
780.688
790.00473
80.0627
800.935
810.543
820.419
830.877
840.67
850.0947
860.948
870.282
880.883
890.0271
90.469
900.433
910.514
920.0386
930.995
940.385
950.225
960.803
970.204
980.0591
990.00312



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: CNhs12374


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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