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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000075,CL:0000144,CL:0000255,CL:0000306,CL:0000325,CL:0000548,CL:0002222,CL:0002224,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000075,CL:0000144,CL:0000255,CL:0000306,CL:0000325,CL:0000548,CL:0002222,CL:0002224,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120

Revision as of 16:51, 29 March 2012


Name:lens epithelial cell line:SRA 01/04
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
sexmale
age3 months
cell typelens epithelial cell
cell lineSRA 01/04
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
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-0.0925
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-lymphoma0.419
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11750

Jaspar motifP-value
MA0002.20.0267
MA0003.10.545
MA0004.10.0865
MA0006.10.728
MA0007.10.728
MA0009.10.699
MA0014.10.127
MA0017.10.0986
MA0018.20.907
MA0019.10.165
MA0024.11.94636e-8
MA0025.10.452
MA0027.10.968
MA0028.10.309
MA0029.10.471
MA0030.10.123
MA0031.10.925
MA0035.20.402
MA0038.14.46942e-5
MA0039.20.184
MA0040.10.865
MA0041.10.0625
MA0042.10.212
MA0043.10.336
MA0046.10.537
MA0047.20.516
MA0048.10.615
MA0050.12.61657e-4
MA0051.10.00286
MA0052.10.022
MA0055.10.283
MA0057.10.527
MA0058.10.159
MA0059.10.539
MA0060.18.06324e-6
MA0061.10.197
MA0062.20.405
MA0065.20.124
MA0066.10.769
MA0067.10.117
MA0068.10.542
MA0069.10.0634
MA0070.10.734
MA0071.10.365
MA0072.10.28
MA0073.10.707
MA0074.10.956
MA0076.10.154
MA0077.10.641
MA0078.10.647
MA0079.20.307
MA0080.22.76046e-7
MA0081.10.433
MA0083.10.607
MA0084.10.514
MA0087.10.98
MA0088.10.82
MA0090.10.0376
MA0091.10.214
MA0092.10.437
MA0093.10.0515
MA0099.29.12035e-7
MA0100.10.11
MA0101.10.357
MA0102.20.00231
MA0103.10.417
MA0104.20.809
MA0105.10.0105
MA0106.10.826
MA0107.10.678
MA0108.23.05525e-4
MA0111.10.236
MA0112.27.84827e-4
MA0113.10.814
MA0114.10.344
MA0115.10.749
MA0116.17.32257e-4
MA0117.10.497
MA0119.10.103
MA0122.10.294
MA0124.10.485
MA0125.10.439
MA0131.10.16
MA0135.10.585
MA0136.10.00787
MA0137.20.293
MA0138.20.029
MA0139.10.0587
MA0140.10.972
MA0141.10.235
MA0142.10.839
MA0143.10.241
MA0144.10.129
MA0145.10.215
MA0146.10.2
MA0147.10.841
MA0148.10.935
MA0149.10.683
MA0150.10.763
MA0152.10.916
MA0153.10.855
MA0154.10.0312
MA0155.10.398
MA0156.10.557
MA0157.10.302
MA0159.10.186
MA0160.10.391
MA0162.10.241
MA0163.10.00295
MA0164.10.793
MA0258.10.255
MA0259.10.862



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: CNhs11750

Novel motifP-value
10.0612
100.227
1000.986
1010.328
1020.161
1030.757
1040.81
1050.767
1060.00729
1070.313
1080.791
1090.716
110.248
1100.227
1110.424
1120.123
1130.00403
1140.15
1150.409
1160.0843
1170.3
1180.966
1190.123
120.864
1200.283
1210.327
1220.18
1230.0632
1240.262
1250.554
1260.0687
1270.747
1280.0179
1290.409
130.297
1300.16
1310.0332
1320.502
1330.635
1340.395
1350.00808
1360.857
1370.31
1380.856
1390.0202
140.509
1400.209
1410.956
1420.881
1430.524
1440.983
1450.233
1460.983
1470.456
1481.16048e-4
1490.06
150.397
1500.569
1510.309
1520.131
1530.112
1540.713
1550.283
1560.432
1570.622
1580.273
1590.138
160.43
1600.0311
1610.304
1620.457
1630.767
1640.893
1650.153
1660.673
1670.247
1680.144
1690.0109
170.329
180.59
190.155
20.703
200.257
210.149
220.315
230.81
240.618
250.209
260.801
270.0158
280.52
290.427
30.0728
300.882
310.459
320.171
330.509
340.393
350.402
360.401
370.272
380.659
390.569
40.207
400.868
410.464
420.314
430.123
440.395
450.871
460.1
470.626
480.133
490.241
50.416
500.913
510.802
520.353
530.185
540.877
550.749
560.973
570.296
580.0161
590.0507
60.317
600.0191
610.78
620.0189
630.182
640.204
650.472
660.011
670.421
680.469
690.442
70.339
700.382
710.617
720.491
730.0845
740.897
750.245
760.786
770.201
780.134
790.185
80.152
800.472
810.257
820.00413
830.21
840.567
850.018
860.465
870.634
880.571
890.0402
90.303
900.351
910.555
920.067
930.507
940.576
950.471
960.419
970.205
980.864
990.994



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: CNhs11750


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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