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FF:11690-122I7: 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 17:22, 29 March 2012


Name:Lens 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
tissueeye
dev stageNA
sexNA
ageNA
cell typelens 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 number6756
catalog numberSC6555
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-0.219
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-0.209
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs12572

Jaspar motifP-value
MA0002.20.262
MA0003.10.466
MA0004.10.109
MA0006.10.277
MA0007.10.403
MA0009.10.0642
MA0014.10.0355
MA0017.10.0566
MA0018.20.0409
MA0019.10.349
MA0024.10.0558
MA0025.10.477
MA0027.10.796
MA0028.10.502
MA0029.10.707
MA0030.10.98
MA0031.10.511
MA0035.20.964
MA0038.10.265
MA0039.20.526
MA0040.10.545
MA0041.10.366
MA0042.10.553
MA0043.10.182
MA0046.10.374
MA0047.20.637
MA0048.10.73
MA0050.10.00605
MA0051.10.816
MA0052.10.098
MA0055.10.0597
MA0057.10.853
MA0058.10.0508
MA0059.10.032
MA0060.10.23
MA0061.10.0317
MA0062.20.0315
MA0065.20.00106
MA0066.10.196
MA0067.10.0216
MA0068.10.0537
MA0069.10.956
MA0070.10.82
MA0071.10.131
MA0072.10.902
MA0073.10.776
MA0074.10.134
MA0076.10.595
MA0077.10.482
MA0078.10.422
MA0079.20.613
MA0080.27.40192e-6
MA0081.10.218
MA0083.17.8835e-5
MA0084.10.897
MA0087.10.766
MA0088.10.0497
MA0090.12.98753e-4
MA0091.10.967
MA0092.10.905
MA0093.10.148
MA0099.20.745
MA0100.10.994
MA0101.10.536
MA0102.20.0765
MA0103.10.0243
MA0104.20.0115
MA0105.13.59916e-4
MA0106.10.442
MA0107.10.285
MA0108.24.86122e-5
MA0111.10.272
MA0112.23.95966e-4
MA0113.10.692
MA0114.10.0243
MA0115.10.0381
MA0116.12.17276e-4
MA0117.10.529
MA0119.10.236
MA0122.10.479
MA0124.10.483
MA0125.10.997
MA0131.10.645
MA0135.10.266
MA0136.11.31105e-7
MA0137.20.751
MA0138.20.204
MA0139.10.475
MA0140.10.903
MA0141.10.015
MA0142.10.859
MA0143.10.793
MA0144.10.751
MA0145.10.992
MA0146.10.00867
MA0147.10.0162
MA0148.10.598
MA0149.10.06
MA0150.10.168
MA0152.10.247
MA0153.10.166
MA0154.10.0801
MA0155.10.552
MA0156.10.00126
MA0157.10.649
MA0159.10.101
MA0160.10.0104
MA0162.10.368
MA0163.17.85861e-6
MA0164.10.952
MA0258.15.53173e-4
MA0259.10.218



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: CNhs12572

Novel motifP-value
10.0251
100.0316
1000.288
1010.574
1020.168
1030.698
1040.809
1050.982
1060.272
1070.901
1080.747
1090.0301
110.0257
1100.141
1110.00572
1120.0769
1130.0894
1140.135
1150.382
1160.482
1170.0321
1180.0324
1190.206
120.317
1200.779
1210.915
1220.867
1232.29713e-6
1240.944
1250.149
1260.424
1270.433
1280.474
1290.179
130.0646
1300.226
1310.395
1320.908
1330.0266
1340.597
1350.403
1360.89
1370.141
1380.561
1390.0971
140.491
1400.356
1410.0344
1420.913
1430.931
1440.868
1450.189
1460.929
1470.403
1480.0295
1490.55
150.324
1500.833
1510.301
1520.701
1530.996
1540.923
1556.20634e-4
1560.162
1570.357
1580.00259
1590.403
160.508
1600.161
1610.245
1620.737
1630.0528
1640.127
1650.564
1660.125
1670.156
1680.904
1690.0176
170.357
180.459
190.403
20.89
200.262
210.0957
220.364
230.747
240.576
250.279
260.00874
270.827
280.899
290.0974
30.124
300.295
310.99
320.349
330.181
340.851
350.226
360.0277
370.228
380.151
390.589
40.593
400.0243
410.295
420.38
430.12
440.293
450.778
460.0596
470.0419
480.121
490.0348
50.754
500.791
510.517
520.981
530.209
540.611
550.894
560.614
570.27
580.145
590.403
60.174
600.143
610.162
620.137
630.2
640.114
650.222
660.571
670.973
680.665
690.895
70.242
700.0393
710.0382
720.844
730.25
740.192
750.012
760.0511
770.244
780.301
790.817
80.2
800.17
810.301
820.156
830.58
840.769
850.27
860.593
870.789
880.932
890.639
90.898
900.279
910.962
920.832
930.553
940.188
950.0403
960.0784
970.319
980.0278
990.569



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: CNhs12572


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)
0000075 (columnar/cuboidal epithelial cell)
0000255 (eukaryotic cell)
0000306 (crystallin accumulating cell)
0000325 (stuff accumulating cell)
0000548 (animal cell)
0002222 (vertebrate lens cell)
0002224 (lens epithelial cell)
0002371 (somatic cell)

UBERON: Anatomy
0000019 (camera-type eye)
0000020 (sense organ)
0000033 (head)
0000047 (simple eye)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000076 (external ectoderm)
0000119 (cell layer)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000484 (simple cuboidal epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000965 (lens of camera-type eye)
0000970 (eye)
0001032 (sensory system)
0001048 (primordium)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001801 (anterior segment of eyeball)
0001803 (epithelium of lens)
0002050 (embryonic structure)
0002104 (visual system)
0002532 (epiblast (generic))
0002546 (cranial placode)
0003073 (lens placode)
0004121 (ectoderm-derived structure)
0004456 (entire sense organ system)
0005085 (ectodermal placode)
0005389 (transparent eye structure)
0005423 (developing anatomical structure)
0005426 (lens vesicle)
0007625 (pigment epithelium of eye)

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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