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{{f5samples
{{f5samples
|id=FF:11526-119I5
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|name=Corneal Epithelial Cells, donor1
|sample_id=11526
|rna_tube_id=119I5
|rna_box=119
|rna_position=I5
|sample_cell_lot=N/A
|sample_cell_catalog=lot:4976
|sample_company=Sciencell/3H
|rna_lot_number=
|rna_catalog_number=SC6515
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=eye
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|sample_sex=
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|sample_ethnicity=
|rna_rin=9.5
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=corneal epithelial cell
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=10
|rna_concentration=1.12
|sample_note=
|profile_hcage=CNhs11336,LSID768,release014,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=SRhi10015,,,
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000144,CL:0000220,CL:0000221,CL:0000255,CL:0000548,CL:0000575,CL:0002077,CL:0002159,CL:0002321,CL:0002371
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|ancestors_in_disease_facet=
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|sample_description=
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|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:11526-119I5
|is_a=EFO:0002091;;FF:0000002;;FF:0000043;;FF:0000210
|is_a=EFO:0002091;;FF:0000002;;FF:0000043;;FF:0000210
|name=Corneal Epithelial Cells, donor1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11336,LSID768,release014,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=SRhi10015,,,
|rna_box=119
|rna_catalog_number=SC6515
|rna_concentration=1.12
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=I5
|rna_rin=9.5
|rna_sample_type=total RNA
|rna_tube_id=119I5
|rna_weight_ug=10
|sample_age=
|sample_cell_catalog=lot:4976
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_type=corneal epithelial cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Sciencell/3H
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11526
|sample_note=
|sample_sex=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=eye
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}}
}}

Revision as of 14:57, 21 March 2012


Name:Corneal Epithelial 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
tissueeye
dev stageNA
sexNA
ageNA
cell typecorneal 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 numberSC6515
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





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-0.0941
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-0.165
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs11336

Jaspar motifP-value
MA0002.20.404
MA0003.10.373
MA0004.10.887
MA0006.10.252
MA0007.10.34
MA0009.10.244
MA0014.10.697
MA0017.10.0965
MA0018.20.0241
MA0019.10.654
MA0024.10.0753
MA0025.10.899
MA0027.10.575
MA0028.10.0713
MA0029.10.338
MA0030.10.703
MA0031.10.0814
MA0035.20.0622
MA0038.10.871
MA0039.20.013
MA0040.10.448
MA0041.10.239
MA0042.10.804
MA0043.10.0635
MA0046.10.0611
MA0047.20.703
MA0048.10.817
MA0050.14.54933e-5
MA0051.10.00133
MA0052.10.791
MA0055.10.187
MA0057.10.0108
MA0058.10.534
MA0059.10.653
MA0060.10.38
MA0061.10.424
MA0062.20.00286
MA0065.20.0197
MA0066.10.283
MA0067.10.11
MA0068.10.0109
MA0069.10.957
MA0070.10.155
MA0071.10.636
MA0072.10.999
MA0073.10.789
MA0074.10.702
MA0076.10.00899
MA0077.10.4
MA0078.10.643
MA0079.20.398
MA0080.23.41451e-4
MA0081.10.0605
MA0083.10.914
MA0084.10.0183
MA0087.10.477
MA0088.10.781
MA0090.10.0114
MA0091.10.871
MA0092.10.407
MA0093.10.766
MA0099.22.37585e-9
MA0100.10.0998
MA0101.10.991
MA0102.20.0917
MA0103.11.70392e-5
MA0104.20.916
MA0105.10.464
MA0106.13.27612e-5
MA0107.10.701
MA0108.20.0061
MA0111.10.75
MA0112.20.0347
MA0113.10.671
MA0114.10.0649
MA0115.10.787
MA0116.10.181
MA0117.10.403
MA0119.10.171
MA0122.10.802
MA0124.10.971
MA0125.10.124
MA0131.10.209
MA0135.10.0152
MA0136.10.00267
MA0137.20.0363
MA0138.20.0794
MA0139.10.52
MA0140.10.941
MA0141.10.25
MA0142.10.207
MA0143.10.645
MA0144.10.742
MA0145.10.0561
MA0146.10.0528
MA0147.10.861
MA0148.10.328
MA0149.10.0327
MA0150.10.507
MA0152.10.0618
MA0153.10.123
MA0154.10.118
MA0155.10.247
MA0156.10.00471
MA0157.10.125
MA0159.10.297
MA0160.10.261
MA0162.10.171
MA0163.10.315
MA0164.10.465
MA0258.10.207
MA0259.10.638



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: CNhs11336

Novel motifP-value
10.537
100.456
1000.827
1010.174
1020.313
1030.313
1040.465
1050.00903
1060.0494
1070.0286
1080.372
1090.0206
110.141
1100.166
1110.599
1120.353
1130.536
1140.438
1150.503
1160.396
1170.762
1180.663
1190.124
120.212
1200.438
1210.266
1220.0479
1230.593
1240.852
1250.566
1260.599
1270.107
1280.187
1290.0104
130.113
1300.547
1310.466
1320.154
1330.0133
1340.873
1350.77
1360.806
1370.444
1380.839
1390.8
140.522
1400.855
1410.745
1420.175
1430.812
1440.753
1450.164
1460.029
1470.169
1480.29
1490.331
150.793
1500.328
1510.37
1520.0957
1530.993
1540.659
1550.668
1560.111
1570.215
1580.582
1590.98
160.127
1600.0318
1610.251
1620.345
1630.645
1640.894
1650.474
1660.413
1670.0996
1680.661
1690.0782
170.127
180.104
190.425
20.105
200.633
210.843
220.154
230.215
240.177
250.947
260.184
270.277
280.922
290.719
30.484
300.111
310.572
320.551
330.288
340.319
350.426
360.801
370.432
380.209
390.155
40.117
400.0161
410.944
420.539
430.343
440.343
450.0976
460.354
470.342
480.17
490.428
50.961
500.416
510.441
520.336
530.994
540.512
550.743
560.281
570.354
580.812
590.0551
60.322
600.166
610.67
620.985
630.149
640.194
650.0606
660.606
670.478
680.655
690.16
70.46
700.0263
710.281
720.572
730.0871
740.109
750.447
760.46
770.0266
780.189
790.8
80.165
800.602
811
820.805
830.993
840.582
850.321
860.781
870.207
880.315
890.034
90.474
900.29
910.246
920.483
930.717
940.404
950.266
960.935
970.856
980.263
990.0211



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: CNhs11336


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)
0000076 (squamous epithelial cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000575 (corneal epithelial cell)
0002077 (ecto-epithelial cell)
0002159 (general ecto-epithelial cell)
0002321 (embryonic 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)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000964 (cornea)
0000970 (eye)
0001032 (sensory system)
0001048 (primordium)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001801 (anterior segment of eyeball)
0002050 (embryonic structure)
0002104 (visual system)
0002342 (neural crest)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0003075 (neural plate)
0003102 (surface structure)
0004121 (ectoderm-derived structure)
0004456 (entire sense organ system)
0005423 (developing anatomical structure)
0005427 (corneal primordium)
0006598 (presumptive structure)
0007284 (presumptive neural plate)

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