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FF:12240-129G8: 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:chorionic membrane cells, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuechorion
dev stageNA
sexNA
ageNA
cell typeunclassifiable
cell lineNA
companyNA
collaborationHiroo Toyoda (Tokyo University of Pharm and life sciences)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-0.291
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs12380

Jaspar motifP-value
MA0002.20.927
MA0003.10.251
MA0004.10.417
MA0006.10.293
MA0007.10.322
MA0009.10.835
MA0014.10.289
MA0017.10.484
MA0018.20.042
MA0019.10.0618
MA0024.10.00192
MA0025.10.674
MA0027.10.91
MA0028.10.0676
MA0029.10.484
MA0030.10.526
MA0031.10.0615
MA0035.20.972
MA0038.10.0229
MA0039.20.642
MA0040.10.825
MA0041.10.818
MA0042.10.958
MA0043.10.0231
MA0046.10.0555
MA0047.20.0251
MA0048.10.477
MA0050.10.0741
MA0051.10.187
MA0052.10.403
MA0055.10.548
MA0057.10.509
MA0058.10.466
MA0059.10.822
MA0060.18.64811e-8
MA0061.10.202
MA0062.20.00168
MA0065.20.0423
MA0066.10.125
MA0067.10.149
MA0068.10.198
MA0069.10.99
MA0070.10.824
MA0071.10.967
MA0072.10.541
MA0073.10.883
MA0074.10.312
MA0076.10.00564
MA0077.10.258
MA0078.10.787
MA0079.20.332
MA0080.20.673
MA0081.10.407
MA0083.10.654
MA0084.10.934
MA0087.10.768
MA0088.10.446
MA0090.13.94883e-4
MA0091.10.232
MA0092.10.207
MA0093.10.296
MA0099.20.0162
MA0100.10.171
MA0101.10.821
MA0102.20.772
MA0103.10.00217
MA0104.20.206
MA0105.10.0212
MA0106.10.301
MA0107.10.452
MA0108.20.00279
MA0111.10.349
MA0112.24.53127e-4
MA0113.10.169
MA0114.10.0957
MA0115.10.453
MA0116.10.00936
MA0117.10.956
MA0119.10.487
MA0122.10.861
MA0124.10.916
MA0125.10.715
MA0131.10.759
MA0135.10.0965
MA0136.10.136
MA0137.20.524
MA0138.20.658
MA0139.10.205
MA0140.10.972
MA0141.10.765
MA0142.10.0606
MA0143.10.205
MA0144.10.0142
MA0145.10.0499
MA0146.10.484
MA0147.10.575
MA0148.10.0612
MA0149.10.661
MA0150.10.791
MA0152.10.0584
MA0153.10.955
MA0154.10.00908
MA0155.10.35
MA0156.10.12
MA0157.10.147
MA0159.10.0457
MA0160.10.618
MA0162.10.0907
MA0163.10.0121
MA0164.10.52
MA0258.10.0679
MA0259.10.891



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: CNhs12380

Novel motifP-value
10.149
100.344
1000.956
1010.514
1020.597
1030.0413
1040.789
1050.418
1060.00651
1070.0105
1080.104
1090.0394
110.193
1100.067
1110.427
1120.108
1130.00221
1140.072
1150.814
1160.39
1170.0826
1180.0569
1190.0695
120.345
1200.0139
1210.832
1220.279
1230.187
1240.359
1250.566
1260.293
1270.542
1280.144
1290.272
130.124
1300.0733
1310.483
1320.202
1330.274
1340.21
1350.487
1360.229
1370.742
1380.398
1390.331
140.93
1400.714
1410.967
1420.381
1430.856
1440.661
1450.201
1460.43
1470.378
1480.457
1490.103
150.156
1500.174
1510.309
1520.0769
1530.471
1540.833
1550.32
1560.691
1570.55
1580.157
1590.72
160.0503
1600.136
1610.52
1620.623
1630.641
1640.236
1650.228
1660.802
1670.872
1680.57
1690.0163
170.0534
180.246
190.0646
20.431
200.89
210.763
220.282
230.00946
240.946
250.664
260.153
270.253
280.841
290.151
30.132
300.266
310.494
320.00688
330.417
340.81
350.439
360.521
370.146
380.503
390.284
40.706
400.069
410.774
420.908
430.14
440.0449
450.276
460.118
470.746
480.451
490.365
50.258
500.618
510.388
520.3
530.491
540.739
550.0469
560.749
570.251
580.73
590.0554
60.77
600.048
610.853
620.3
630.423
640.426
650.0883
660.103
670.648
680.73
690.513
70.21
700.0116
710.105
720.326
730.126
740.849
750.157
760.79
770.032
780.314
790.143
80.218
800.831
810.438
820.0857
830.548
840.127
850.00658
860.924
870.354
880.606
890.0806
90.477
900.51
910.375
920.23
930.96
940.125
950.398
960.95
970.194
980.441
990.446



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: CNhs12380


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)
0002541 (chorionic membrane mesenchymal stem cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000158 (membranous layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000476 (acellular anatomical structure)
0000478 (extraembryonic structure)
0000479 (tissue)
0000480 (anatomical group)
0000920 (egg chorion)
0001062 (anatomical entity)
0002384 (connective tissue)
0003124 (chorion)
0004923 (organ component layer)
0005631 (extraembryonic membrane)

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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