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FF:12239-129G7: 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, donor2
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-penis-0.1
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-lymphoma0.0996
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: CNhs12506

Jaspar motifP-value
MA0002.20.114
MA0003.10.324
MA0004.10.0848
MA0006.10.00509
MA0007.10.767
MA0009.10.871
MA0014.10.627
MA0017.10.157
MA0018.20.0166
MA0019.10.12
MA0024.10.283
MA0025.10.12
MA0027.10.373
MA0028.10.479
MA0029.10.347
MA0030.10.957
MA0031.10.503
MA0035.20.727
MA0038.10.429
MA0039.20.637
MA0040.10.511
MA0041.10.541
MA0042.10.568
MA0043.10.00151
MA0046.10.454
MA0047.20.402
MA0048.10.584
MA0050.10.829
MA0051.10.496
MA0052.10.12
MA0055.10.617
MA0057.10.93
MA0058.10.0319
MA0059.10.00502
MA0060.10.0121
MA0061.10.0195
MA0062.20.00256
MA0065.20.396
MA0066.10.339
MA0067.17.147e-4
MA0068.10.0437
MA0069.10.8
MA0070.10.862
MA0071.10.557
MA0072.10.781
MA0073.10.902
MA0074.10.348
MA0076.10.381
MA0077.10.953
MA0078.10.487
MA0079.20.255
MA0080.21.17241e-6
MA0081.10.0237
MA0083.17.64567e-5
MA0084.10.138
MA0087.10.498
MA0088.10.449
MA0090.11.06921e-8
MA0091.10.0867
MA0092.10.105
MA0093.10.104
MA0099.20.389
MA0100.10.565
MA0101.10.00293
MA0102.20.24
MA0103.10.28
MA0104.23.60811e-5
MA0105.10.0238
MA0106.10.242
MA0107.10.0131
MA0108.21.51129e-8
MA0111.10.797
MA0112.20.0807
MA0113.10.436
MA0114.10.487
MA0115.10.444
MA0116.10.0614
MA0117.10.236
MA0119.10.112
MA0122.10.405
MA0124.10.657
MA0125.10.64
MA0131.10.318
MA0135.10.42
MA0136.12.57729e-6
MA0137.20.757
MA0138.20.594
MA0139.10.981
MA0140.10.371
MA0141.10.0709
MA0142.10.153
MA0143.10.787
MA0144.10.276
MA0145.10.2
MA0146.10.952
MA0147.11.00713e-4
MA0148.10.999
MA0149.10.553
MA0150.10.00494
MA0152.10.141
MA0153.10.186
MA0154.10.701
MA0155.10.348
MA0156.15.19486e-4
MA0157.10.703
MA0159.10.891
MA0160.10.376
MA0162.10.0882
MA0163.10.229
MA0164.10.695
MA0258.10.918
MA0259.10.0249



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: CNhs12506

Novel motifP-value
10.136
100.124
1000.151
1010.206
1020.632
1030.934
1040.758
1050.397
1060.684
1070.0587
1080.64
1090.331
110.35
1100.934
1110.0157
1120.567
1130.762
1140.283
1150.249
1160.767
1170.757
1180.646
1190.287
120.744
1200.294
1210.739
1220.401
1231.49846e-4
1240.0438
1250.689
1260.625
1270.514
1280.612
1290.407
130.572
1300.417
1310.489
1320.28
1330.178
1340.685
1350.415
1360.248
1370.0592
1380.516
1390.0317
140.54
1400.412
1410.364
1420.724
1430.553
1440.36
1450.918
1460.636
1470.629
1480.403
1490.115
150.359
1500.254
1510.836
1520.00254
1530.699
1540.559
1550.299
1560.519
1570.407
1580.327
1590.766
160.127
1600.534
1610.251
1620.401
1630.803
1640.566
1650.368
1660.534
1670.26
1680.371
1690.275
170.718
180.737
190.16
20.0839
200.368
210.953
220.59
230.816
240.904
250.392
260.301
270.586
280.514
290.434
30.498
300.0436
310.76
328.94203e-7
330.626
340.275
350.225
360.0541
370.561
380.571
390.215
40.733
400.333
410.127
420.383
430.309
440.479
450.125
460.402
470.398
480.545
490.124
50.512
500.588
510.949
520.716
530.2
540.82
550.682
560.829
570.699
580.0806
590.25
60.271
600.659
610.883
620.126
630.664
640.422
650.963
660.518
670.732
680.332
690.43
70.503
700.281
710.0455
720.996
730.00408
740.203
750.653
760.365
770.0664
780.821
790.0797
80.636
800.529
810.151
820.752
830.38
840.11
850.969
860.876
870.103
880.941
890.696
90.863
900.418
910.512
920.312
930.659
940.42
950.175
960.179
970.467
980.394
990.0594



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: CNhs12506


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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