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FF:11323-117D9: 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 17:03, 29 March 2012


Name:Ciliary Epithelial Cells, donor2
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 stagefetus
sexunknown
agefetal
cell typeciliated 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 number564
catalog numberSC6585
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]


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-penis0.0764
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-lymphoma0.166
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
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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: CNhs11966

Jaspar motifP-value
MA0002.20.0131
MA0003.10.0331
MA0004.10.052
MA0006.10.342
MA0007.10.604
MA0009.10.147
MA0014.10.197
MA0017.10.0127
MA0018.20.0439
MA0019.10.843
MA0024.10.127
MA0025.10.138
MA0027.10.9
MA0028.10.587
MA0029.10.445
MA0030.18.68829e-4
MA0031.15.15352e-5
MA0035.20.0388
MA0038.10.101
MA0039.20.418
MA0040.10.405
MA0041.10.198
MA0042.10.255
MA0043.10.0163
MA0046.10.73
MA0047.24.41231e-5
MA0048.10.0833
MA0050.13.99191e-4
MA0051.10.0127
MA0052.10.0122
MA0055.10.662
MA0057.10.672
MA0058.10.0104
MA0059.10.0507
MA0060.12.22669e-4
MA0061.11.94578e-4
MA0062.20.0399
MA0065.20.00444
MA0066.10.29
MA0067.10.00516
MA0068.10.0264
MA0069.10.622
MA0070.10.811
MA0071.10.314
MA0072.10.509
MA0073.10.99
MA0074.10.427
MA0076.10.965
MA0077.10.139
MA0078.10.563
MA0079.20.465
MA0080.22.2974e-13
MA0081.10.0363
MA0083.10.0121
MA0084.10.317
MA0087.10.266
MA0088.10.113
MA0090.10.0163
MA0091.10.163
MA0092.10.274
MA0093.10.0691
MA0099.22.88005e-5
MA0100.10.927
MA0101.10.0123
MA0102.22.72545e-4
MA0103.10.118
MA0104.20.00629
MA0105.12.667e-6
MA0106.10.961
MA0107.11.46473e-4
MA0108.20.775
MA0111.10.587
MA0112.22.93011e-4
MA0113.10.0673
MA0114.10.032
MA0115.10.632
MA0116.11.77111e-5
MA0117.10.575
MA0119.10.771
MA0122.10.974
MA0124.10.503
MA0125.10.412
MA0131.10.912
MA0135.10.623
MA0136.17.8711e-17
MA0137.20.153
MA0138.20.166
MA0139.10.537
MA0140.10.012
MA0141.10.123
MA0142.10.166
MA0143.10.374
MA0144.10.159
MA0145.10.458
MA0146.10.196
MA0147.10.0351
MA0148.15.93989e-4
MA0149.10.0905
MA0150.12.41884e-5
MA0152.10.269
MA0153.10.753
MA0154.10.00243
MA0155.10.51
MA0156.11.84549e-9
MA0157.10.00728
MA0159.10.0204
MA0160.10.0239
MA0162.10.622
MA0163.11.09749e-6
MA0164.10.777
MA0258.10.00549
MA0259.10.223



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: CNhs11966

Novel motifP-value
10.109
100.229
1000.637
1010.498
1020.477
1030.165
1040.656
1050.0522
1060.0419
1070.705
1080.888
1090.108
110.114
1100.704
1110.00601
1120.039
1130.166
1140.115
1150.0361
1160.779
1170.28
1180.46
1190.621
120.193
1200.925
1210.961
1220.33
1230.0816
1240.236
1250.82
1260.101
1270.158
1280.36
1290.335
130.552
1300.492
1310.693
1320.89
1330.904
1340.55
1350.0395
1360.24
1370.0594
1380.24
1390.0577
140.615
1400.164
1410.255
1420.98
1430.0892
1440.771
1450.728
1460.591
1470.539
1480.0382
1490.234
150.116
1500.731
1510.212
1520.182
1530.326
1540.558
1550.012
1560.132
1570.378
1580.00554
1590.544
160.71
1600.265
1610.66
1620.226
1630.437
1640.286
1650.883
1660.0398
1670.946
1680.719
1690.00845
170.215
180.0945
190.498
20.422
200.922
210.769
220.154
230.153
240.334
250.253
260.427
270.27
280.919
290.212
30.237
300.895
310.748
320.302
330.445
340.526
350.318
360.0252
370.206
380.119
390.423
40.494
400.071
410.034
420.319
430.0794
440.925
450.428
460.105
470.378
480.337
490.048
50.123
500.716
510.502
520.438
530.37
540.515
550.989
560.498
570.611
580.0756
590.292
60.644
600.0376
610.169
620.0704
630.235
640.204
650.134
660.848
670.832
680.489
690.767
70.29
700.0924
710.144
720.103
730.128
740.64
750.0293
760.197
770.261
780.718
790.536
80.563
800.105
810.483
820.0919
830.579
840.27
850.0489
860.165
870.799
880.743
890.575
90.261
900.516
910.856
920.201
930.0062
940.145
950.0203
960.0499
970.782
980.0547
990.156



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: CNhs11966


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)
0000064 (ciliated cell)
0000066 (epithelial cell)
0000067 (ciliated epithelial cell)
0000075 (columnar/cuboidal epithelial cell)
0000133 (neurectodermal cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000710 (neurecto-epithelial cell)
0002077 (ecto-epithelial cell)
0002304 (non-pigmented ciliary epithelial cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0005012 (multi-ciliated epithelial 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)
0000119 (cell layer)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000488 (atypical epithelium)
0000970 (eye)
0001009 (circulatory system)
0001032 (sensory system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001768 (uvea)
0001775 (ciliary body)
0001778 (ciliary epithelium)
0001801 (anterior segment of eyeball)
0002049 (vasculature)
0002104 (visual system)
0002200 (vasculature of head)
0002203 (vasculature of eye)
0004456 (entire sense organ system)
0004535 (cardiovascular system)
0006876 (vasculature of organ)
0007625 (pigment epithelium of eye)
0007798 (vascular system)

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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