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FF:11694-123A2: 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 17:12, 29 March 2012


Name:Amniotic Epithelial 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
tissueamnion
dev stageNA
sexNA
ageNA
cell typeamniotic epithelial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC7105
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-0.0168
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-0.0972
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: CNhs12125

Jaspar motifP-value
MA0002.20.683
MA0003.10.329
MA0004.10.603
MA0006.10.0699
MA0007.10.0117
MA0009.10.607
MA0014.10.747
MA0017.10.66
MA0018.20.0151
MA0019.10.242
MA0024.10.141
MA0025.10.0257
MA0027.10.733
MA0028.10.0225
MA0029.10.0672
MA0030.10.0203
MA0031.10.0169
MA0035.20.228
MA0038.10.339
MA0039.20.126
MA0040.10.302
MA0041.10.75
MA0042.10.415
MA0043.17.24482e-4
MA0046.10.798
MA0047.20.424
MA0048.10.96
MA0050.11.80754e-6
MA0051.11.24616e-6
MA0052.10.569
MA0055.10.0446
MA0057.10.336
MA0058.10.281
MA0059.10.726
MA0060.10.464
MA0061.10.712
MA0062.28.79378e-6
MA0065.20.173
MA0066.10.138
MA0067.10.00613
MA0068.10.208
MA0069.10.401
MA0070.10.0245
MA0071.10.484
MA0072.10.675
MA0073.10.407
MA0074.10.364
MA0076.15.29519e-4
MA0077.10.587
MA0078.10.501
MA0079.20.445
MA0080.24.77093e-8
MA0081.17.38018e-4
MA0083.10.768
MA0084.10.298
MA0087.10.842
MA0088.10.567
MA0090.11.99227e-4
MA0091.10.197
MA0092.10.304
MA0093.10.47
MA0099.20.00121
MA0100.10.24
MA0101.10.167
MA0102.22.042e-4
MA0103.10.00339
MA0104.20.144
MA0105.10.89
MA0106.10.228
MA0107.10.115
MA0108.20.291
MA0111.10.613
MA0112.20.016
MA0113.10.00699
MA0114.10.324
MA0115.10.304
MA0116.10.534
MA0117.10.288
MA0119.10.221
MA0122.10.94
MA0124.10.771
MA0125.10.335
MA0131.10.452
MA0135.10.696
MA0136.18.98397e-10
MA0137.20.00426
MA0138.20.424
MA0139.10.914
MA0140.10.595
MA0141.10.354
MA0142.10.682
MA0143.10.25
MA0144.10.986
MA0145.10.143
MA0146.10.0327
MA0147.10.259
MA0148.10.976
MA0149.10.816
MA0150.10.481
MA0152.10.871
MA0153.10.46
MA0154.10.277
MA0155.10.126
MA0156.16.95269e-7
MA0157.10.0152
MA0159.10.323
MA0160.10.784
MA0162.10.0399
MA0163.10.168
MA0164.10.143
MA0258.10.0877
MA0259.10.141



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: CNhs12125

Novel motifP-value
10.806
100.781
1000.758
1010.641
1020.75
1030.21
1040.868
1050.252
1060.00442
1070.0102
1080.119
1090.0553
110.255
1100.138
1110.701
1120.779
1130.00653
1140.575
1150.567
1160.412
1170.34
1180.433
1190.155
120.952
1200.191
1210.553
1220.741
1230.664
1240.239
1250.505
1260.407
1270.505
1280.0847
1290.407
130.341
1300.631
1310.0168
1320.177
1330.298
1340.21
1350.496
1360.554
1370.113
1380.616
1390.871
140.792
1400.282
1410.674
1420.154
1430.828
1440.558
1450.441
1460.113
1470.156
1480.161
1490.0673
150.83
1500.221
1510.256
1520.0272
1530.212
1540.757
1550.467
1560.437
1570.415
1580.723
1590.539
160.0677
1600.0635
1610.307
1620.202
1630.93
1640.708
1650.998
1660.644
1670.273
1680.524
1690.0468
170.0672
180.147
190.272
20.0957
200.919
210.803
220.159
230.115
240.676
250.96
260.152
270.306
280.915
290.492
30.56
300.22
310.499
321.30338e-6
330.518
340.367
350.359
360.299
370.336
380.436
390.224
40.514
400.0368
410.996
420.83
430.196
440.217
450.138
460.334
470.669
480.201
490.194
50.928
500.404
510.215
520.224
530.821
540.226
550.132
560.32
570.459
580.7
590.0605
60.485
600.305
610.709
620.928
630.298
640.139
650.161
660.328
670.429
680.276
690.00233
70.613
700.0572
710.379
720.83
730.0339
740.0741
750.392
760.446
770.0165
780.496
790.0455
80.2
800.909
810.908
820.354
830.756
840.411
850.118
860.657
870.627
880.167
890.129
90.46
900.13
910.0987
920.456
930.5
940.398
950.144
960.918
970.341
980.591
990.00677



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: CNhs12125


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002371 (somatic cell)
0002536 (amniotic epithelial cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000158 (membranous layer)
0000305 (amnion)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000478 (extraembryonic structure)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004871 (somatic layer of lateral plate mesoderm)
0004923 (organ component layer)
0005423 (developing anatomical structure)
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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