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FF:11530-119I9: 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 17:23, 29 March 2012


Name:Iris Pigment 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 typeiris pigment 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 numberSC6565
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-penis-0.0293
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-lymphoma0.172
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
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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: CNhs12596

Jaspar motifP-value
MA0002.20.582
MA0003.10.655
MA0004.10.0743
MA0006.10.287
MA0007.10.638
MA0009.10.203
MA0014.10.795
MA0017.10.438
MA0018.24.21501e-5
MA0019.10.739
MA0024.10.581
MA0025.10.132
MA0027.10.937
MA0028.10.616
MA0029.10.17
MA0030.10.0304
MA0031.10.00798
MA0035.20.16
MA0038.10.106
MA0039.20.454
MA0040.10.816
MA0041.10.543
MA0042.10.729
MA0043.10.00227
MA0046.10.751
MA0047.20.0506
MA0048.10.195
MA0050.11.45519e-5
MA0051.10.0224
MA0052.10.0256
MA0055.10.877
MA0057.10.582
MA0058.10.00817
MA0059.10.692
MA0060.12.71236e-4
MA0061.15.3721e-5
MA0062.24.42295e-5
MA0065.20.158
MA0066.10.934
MA0067.15.43075e-4
MA0068.10.326
MA0069.10.949
MA0070.10.346
MA0071.10.216
MA0072.10.592
MA0073.10.955
MA0074.10.462
MA0076.10.134
MA0077.10.851
MA0078.10.496
MA0079.20.0919
MA0080.24.73332e-10
MA0081.10.0187
MA0083.10.0562
MA0084.10.925
MA0087.10.82
MA0088.10.142
MA0090.13.68051e-5
MA0091.10.227
MA0092.10.601
MA0093.10.0826
MA0099.20.00137
MA0100.10.433
MA0101.14.98217e-4
MA0102.20.768
MA0103.10.0446
MA0104.20.111
MA0105.10.0835
MA0106.10.711
MA0107.17.79496e-6
MA0108.25.73316e-4
MA0111.10.357
MA0112.20.242
MA0113.10.351
MA0114.10.612
MA0115.10.655
MA0116.10.501
MA0117.10.104
MA0119.10.0746
MA0122.10.946
MA0124.10.664
MA0125.10.428
MA0131.10.875
MA0135.10.931
MA0136.14.63344e-6
MA0137.20.569
MA0138.20.162
MA0139.10.625
MA0140.10.245
MA0141.10.407
MA0142.10.155
MA0143.10.614
MA0144.10.463
MA0145.10.198
MA0146.10.154
MA0147.10.257
MA0148.10.554
MA0149.10.253
MA0150.10.0985
MA0152.10.0452
MA0153.10.957
MA0154.10.84
MA0155.10.977
MA0156.11.15427e-6
MA0157.10.266
MA0159.10.571
MA0160.10.0539
MA0162.10.264
MA0163.10.373
MA0164.10.809
MA0258.10.0165
MA0259.10.174



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: CNhs12596

Novel motifP-value
10.272
100.0301
1000.98
1010.6
1020.156
1030.788
1040.825
1050.553
1060.419
1070.0551
1080.842
1090.0916
110.272
1100.547
1110.0623
1120.0179
1130.0323
1140.296
1150.759
1160.977
1170.00589
1180.413
1190.539
120.247
1200.462
1210.971
1220.375
1232.31896e-4
1240.602
1250.912
1260.318
1270.702
1280.728
1290.329
130.649
1300.134
1310.633
1320.872
1330.635
1340.899
1350.497
1360.58
1370.0623
1380.396
1390.0389
140.447
1400.18
1410.0737
1420.137
1430.947
1440.63
1450.607
1460.979
1470.289
1480.509
1490.307
150.636
1500.548
1510.187
1520.651
1530.881
1540.85
1557.66109e-4
1560.425
1570.355
1580.00153
1590.65
160.837
1600.561
1610.386
1620.128
1630.281
1640.0496
1650.861
1660.0746
1670.541
1680.933
1690.851
170.475
180.526
190.842
20.826
200.435
210.486
220.411
230.843
240.333
250.115
260.531
270.776
280.43
290.216
30.314
300.4
310.774
320.459
330.357
340.901
350.404
360.213
370.247
380.157
390.224
40.783
400.721
410.0164
420.463
430.141
440.68
450.846
460.457
470.294
480.517
490.112
50.657
500.995
510.623
520.776
530.182
540.518
550.92
560.964
570.876
580.126
590.594
60.407
600.123
610.285
620.102
630.608
640.474
650.115
660.344
670.725
680.74
690.499
70.312
700.0698
710.21
720.883
730.0883
740.561
750.0132
760.0294
770.944
780.921
790.408
80.834
800.606
810.926
820.0531
830.265
840.762
850.271
860.183
870.494
880.923
890.779
90.971
900.616
910.926
920.662
930.164
940.93
950.0382
960.524
970.973
980.116
990.0154



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: CNhs12596


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)
0000147 (pigment cell)
0000255 (eukaryotic cell)
0000325 (stuff accumulating cell)
0000342 (pigment cell (sensu Vertebrata))
0000548 (animal cell)
0002565 (iris pigment 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)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000970 (eye)
0001009 (circulatory system)
0001032 (sensory system)
0001048 (primordium)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001768 (uvea)
0001769 (iris)
0001801 (anterior segment of eyeball)
0002049 (vasculature)
0002050 (embryonic structure)
0002104 (visual system)
0002200 (vasculature of head)
0002203 (vasculature of eye)
0002346 (neurectoderm)
0002506 (iris epithelium)
0002532 (epiblast (generic))
0003056 (pre-chordal neural plate)
0003071 (eye primordium)
0003075 (neural plate)
0004121 (ectoderm-derived structure)
0004128 (optic vesicle)
0004456 (entire sense organ system)
0004535 (cardiovascular system)
0005085 (ectodermal placode)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0006876 (vasculature of organ)
0007284 (presumptive neural plate)
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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