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FF:11687-122I4: 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:Corneal 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 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-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-penis0.0728
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-lymphoma0.0318
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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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: CNhs12123

Jaspar motifP-value
MA0002.20.961
MA0003.10.443
MA0004.10.922
MA0006.10.242
MA0007.10.416
MA0009.10.184
MA0014.10.64
MA0017.10.0434
MA0018.20.0222
MA0019.10.76
MA0024.10.82
MA0025.10.783
MA0027.10.914
MA0028.10.391
MA0029.10.438
MA0030.10.143
MA0031.10.0392
MA0035.20.116
MA0038.10.576
MA0039.20.011
MA0040.10.242
MA0041.10.284
MA0042.10.82
MA0043.10.0319
MA0046.10.556
MA0047.20.722
MA0048.10.906
MA0050.11.63396e-8
MA0051.15.03483e-5
MA0052.10.949
MA0055.10.141
MA0057.10.00199
MA0058.10.524
MA0059.10.616
MA0060.10.125
MA0061.10.89
MA0062.20.0568
MA0065.20.00289
MA0066.10.0506
MA0067.10.0476
MA0068.10.013
MA0069.10.602
MA0070.10.368
MA0071.10.513
MA0072.10.958
MA0073.10.942
MA0074.10.415
MA0076.10.103
MA0077.10.261
MA0078.10.946
MA0079.20.388
MA0080.21.23991e-6
MA0081.10.047
MA0083.10.168
MA0084.10.0185
MA0087.10.441
MA0088.10.566
MA0090.10.0832
MA0091.10.814
MA0092.10.53
MA0093.10.772
MA0099.29.73211e-6
MA0100.10.158
MA0101.10.329
MA0102.20.0563
MA0103.12.01667e-6
MA0104.20.918
MA0105.10.554
MA0106.13.67716e-7
MA0107.10.335
MA0108.20.0128
MA0111.10.696
MA0112.20.0174
MA0113.10.556
MA0114.10.0414
MA0115.10.528
MA0116.10.0758
MA0117.10.774
MA0119.10.13
MA0122.10.631
MA0124.10.496
MA0125.10.248
MA0131.10.38
MA0135.10.0145
MA0136.12.68889e-4
MA0137.20.00537
MA0138.20.0249
MA0139.10.363
MA0140.10.998
MA0141.10.112
MA0142.10.116
MA0143.10.457
MA0144.10.443
MA0145.10.0673
MA0146.10.0431
MA0147.10.739
MA0148.10.678
MA0149.10.0371
MA0150.10.742
MA0152.10.0895
MA0153.10.662
MA0154.10.131
MA0155.10.292
MA0156.10.00246
MA0157.10.0679
MA0159.10.174
MA0160.10.323
MA0162.10.13
MA0163.10.156
MA0164.10.988
MA0258.10.123
MA0259.10.935



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: CNhs12123

Novel motifP-value
10.275
100.882
1000.595
1010.171
1020.251
1030.127
1040.768
1050.0466
1060.0377
1070.0223
1080.374
1090.00232
110.125
1100.127
1110.31
1120.262
1130.319
1140.431
1150.0725
1160.275
1170.385
1180.774
1190.0676
120.619
1200.0396
1210.353
1220.0551
1230.916
1240.419
1250.464
1260.312
1270.11
1280.194
1290.0198
130.0339
1300.611
1310.664
1320.138
1330.0693
1340.628
1350.897
1360.232
1370.207
1380.705
1390.616
140.687
1400.324
1410.451
1420.0547
1430.565
1440.241
1450.177
1460.0318
1470.207
1480.406
1490.527
150.695
1500.364
1510.281
1520.0688
1530.806
1540.734
1550.485
1560.22
1570.45
1580.34
1590.56
160.0487
1600.045
1610.226
1620.234
1630.798
1640.724
1650.642
1660.587
1670.658
1680.735
1690.0407
170.102
180.227
190.394
20.109
200.79
210.495
220.166
230.448
240.0909
250.886
260.0757
270.329
280.898
290.316
30.471
300.129
310.576
320.377
330.251
340.569
350.709
360.778
370.325
380.267
390.168
40.31
400.0106
410.691
420.512
430.337
440.101
450.159
460.228
470.177
480.083
490.432
50.827
500.463
510.537
520.435
530.973
540.571
550.575
560.352
570.256
580.745
590.0436
60.349
600.205
610.542
620.772
630.179
640.177
650.103
660.368
670.717
680.619
690.0488
70.337
700.0273
710.192
720.707
730.0461
740.0544
750.279
760.622
770.0161
780.103
790.628
80.113
800.806
810.843
820.528
830.961
840.523
850.355
860.88
870.0738
880.435
890.0358
90.588
900.109
910.301
920.689
930.811
940.826
950.067
960.864
970.974
980.262
990.00772



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: CNhs12123


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

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