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FF:12238-129G6: 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 17:20, 29 March 2012


Name:chorionic membrane cells, donor1
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
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-0.298
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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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: CNhs12504

Jaspar motifP-value
MA0002.20.191
MA0003.10.375
MA0004.10.584
MA0006.10.0215
MA0007.10.276
MA0009.10.69
MA0014.10.163
MA0017.10.644
MA0018.20.916
MA0019.10.0673
MA0024.10.0012
MA0025.10.845
MA0027.10.895
MA0028.10.0216
MA0029.10.241
MA0030.10.439
MA0031.10.0082
MA0035.20.119
MA0038.10.587
MA0039.20.0014
MA0040.10.988
MA0041.10.64
MA0042.10.858
MA0043.10.516
MA0046.10.331
MA0047.20.0477
MA0048.10.272
MA0050.10.221
MA0051.10.0575
MA0052.10.63
MA0055.10.967
MA0057.10.603
MA0058.10.604
MA0059.10.189
MA0060.10.185
MA0061.10.636
MA0062.22.65394e-4
MA0065.20.423
MA0066.10.254
MA0067.10.169
MA0068.10.00178
MA0069.10.845
MA0070.10.654
MA0071.10.758
MA0072.10.732
MA0073.10.767
MA0074.10.658
MA0076.10.00191
MA0077.10.678
MA0078.10.834
MA0079.20.462
MA0080.20.00278
MA0081.10.0535
MA0083.10.0227
MA0084.10.815
MA0087.10.984
MA0088.10.133
MA0090.14.85758e-8
MA0091.10.951
MA0092.10.157
MA0093.10.528
MA0099.23.39193e-14
MA0100.10.231
MA0101.10.904
MA0102.20.882
MA0103.10.00516
MA0104.20.0732
MA0105.10.957
MA0106.10.485
MA0107.10.397
MA0108.23.03981e-20
MA0111.10.903
MA0112.20.12
MA0113.10.0306
MA0114.10.213
MA0115.10.274
MA0116.10.597
MA0117.10.676
MA0119.10.889
MA0122.10.157
MA0124.10.607
MA0125.10.82
MA0131.10.645
MA0135.10.643
MA0136.16.35747e-4
MA0137.20.716
MA0138.20.862
MA0139.10.824
MA0140.10.81
MA0141.10.166
MA0142.10.918
MA0143.10.624
MA0144.10.0269
MA0145.10.0199
MA0146.10.204
MA0147.10.124
MA0148.10.211
MA0149.10.748
MA0150.10.198
MA0152.10.14
MA0153.10.916
MA0154.10.218
MA0155.10.491
MA0156.14.46787e-4
MA0157.10.0945
MA0159.10.238
MA0160.10.531
MA0162.10.385
MA0163.10.838
MA0164.10.575
MA0258.10.958
MA0259.10.637



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: CNhs12504

Novel motifP-value
10.868
100.793
1000.727
1010.24
1020.686
1030.323
1040.801
1050.188
1060.0023
1070.0101
1080.0511
1090.00939
110.795
1100.267
1110.225
1120.33
1139.02951e-4
1140.928
1150.87
1160.817
1170.269
1180.074
1190.451
120.629
1200.206
1210.673
1220.908
1230.0146
1240.0374
1250.878
1260.193
1270.395
1280.53
1290.764
130.21
1300.392
1310.389
1320.384
1330.114
1340.153
1350.632
1360.019
1370.457
1380.989
1390.842
140.747
1400.522
1410.377
1420.609
1430.462
1440.541
1450.685
1460.434
1470.858
1480.892
1490.392
150.915
1500.11
1510.188
1520.0102
1530.63
1540.722
1550.131
1560.874
1570.739
1580.174
1590.61
160.0381
1600.355
1610.846
1620.721
1630.101
1640.608
1650.589
1660.64
1670.161
1680.932
1690.0849
170.161
180.887
190.139
20.192
200.704
210.363
220.183
230.0536
240.946
250.8
260.451
270.785
280.94
290.368
30.616
300.107
310.702
320.0759
330.529
340.896
350.272
360.606
370.254
380.747
390.155
40.522
400.131
410.465
420.736
430.476
440.595
450.0352
460.859
470.393
480.979
490.794
50.855
500.324
510.917
520.127
530.295
540.953
550.36
560.647
570.714
580.852
590.354
60.996
600.144
610.376
620.954
630.611
640.77
650.409
660.406
670.688
680.536
690.308
70.371
700.203
710.971
720.287
730.015
740.463
750.364
760.734
770.0283
780.533
790.71
80.766
800.802
810.578
820.767
830.884
840.152
850.0472
860.943
870.655
880.566
890.577
90.677
900.448
910.715
920.906
930.825
940.894
950.144
960.727
970.143
980.95
990.98



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: CNhs12504


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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