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FF:11528-119I7: 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 16:46, 29 March 2012


Name:Retinal 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 typeretinal 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 numberSC6545
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-0.022
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-lymphoma0.00114
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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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: CNhs11338

Jaspar motifP-value
MA0002.20.678
MA0003.10.369
MA0004.10.289
MA0006.10.125
MA0007.10.276
MA0009.10.201
MA0014.10.772
MA0017.10.908
MA0018.20.142
MA0019.10.0847
MA0024.10.95
MA0025.10.902
MA0027.10.582
MA0028.10.0789
MA0029.10.56
MA0030.10.314
MA0031.10.226
MA0035.20.00652
MA0038.10.0273
MA0039.20.402
MA0040.10.861
MA0041.10.309
MA0042.10.91
MA0043.10.00391
MA0046.10.017
MA0047.20.0479
MA0048.10.646
MA0050.12.97617e-11
MA0051.12.52686e-7
MA0052.10.0723
MA0055.10.0618
MA0057.10.467
MA0058.10.238
MA0059.10.305
MA0060.11.75584e-6
MA0061.10.0164
MA0062.24.98348e-5
MA0065.20.0939
MA0066.10.324
MA0067.10.0224
MA0068.10.721
MA0069.10.458
MA0070.10.00576
MA0071.10.382
MA0072.10.969
MA0073.10.984
MA0074.10.98
MA0076.10.00432
MA0077.10.0203
MA0078.10.195
MA0079.20.433
MA0080.21.00079e-9
MA0081.10.0311
MA0083.10.828
MA0084.10.00757
MA0087.10.581
MA0088.10.556
MA0090.15.02192e-6
MA0091.10.641
MA0092.10.518
MA0093.10.268
MA0099.20.887
MA0100.10.103
MA0101.10.0214
MA0102.23.23088e-4
MA0103.10.00135
MA0104.20.896
MA0105.10.0854
MA0106.10.744
MA0107.10.00626
MA0108.25.96799e-8
MA0111.10.374
MA0112.20.48
MA0113.10.641
MA0114.10.109
MA0115.10.471
MA0116.10.185
MA0117.10.168
MA0119.10.448
MA0122.10.415
MA0124.10.297
MA0125.10.0883
MA0131.10.023
MA0135.10.0613
MA0136.17.28381e-10
MA0137.20.00935
MA0138.20.471
MA0139.10.883
MA0140.10.285
MA0141.10.27
MA0142.10.723
MA0143.10.674
MA0144.10.0615
MA0145.10.171
MA0146.10.178
MA0147.10.847
MA0148.10.124
MA0149.10.508
MA0150.18.1522e-4
MA0152.10.178
MA0153.10.0499
MA0154.10.674
MA0155.10.02
MA0156.14.23421e-9
MA0157.10.491
MA0159.10.27
MA0160.10.834
MA0162.10.161
MA0163.10.604
MA0164.10.821
MA0258.10.732
MA0259.10.159



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: CNhs11338

Novel motifP-value
10.216
100.0126
1000.9
1010.498
1020.746
1030.963
1040.886
1050.0435
1060.749
1070.0432
1080.691
1090.349
110.703
1100.361
1110.0946
1120.0732
1130.181
1140.521
1150.936
1160.284
1170.185
1180.58
1190.896
120.995
1200.684
1210.535
1220.123
1230.0257
1240.403
1250.0775
1260.158
1270.97
1280.638
1290.947
130.717
1300.152
1310.734
1320.0882
1330.969
1340.777
1350.162
1360.971
1370.157
1380.0127
1390.803
140.408
1400.819
1410.122
1420.656
1430.882
1440.87
1450.631
1460.332
1470.934
1480.18
1490.0788
150.788
1500.667
1510.557
1520.086
1530.415
1540.108
1550.295
1560.445
1570.0205
1580.0416
1590.56
160.454
1600.0771
1610.502
1620.0485
1630.737
1640.0626
1650.0454
1660.951
1670.315
1680.185
1690.296
170.511
180.544
190.821
20.414
200.438
210.379
220.253
230.817
240.88
250.44
260.327
270.391
280.476
290.44
30.318
300.0417
310.874
320.468
330.66
340.111
350.622
360.323
370.643
380.905
390.319
40.456
400.0308
410.119
420.343
430.8
440.67
450.114
460.881
470.83
480.579
490.771
50.435
500.27
510.373
520.545
530.535
540.577
550.474
560.657
570.79
580.244
590.239
60.535
600.533
610.56
620.157
630.119
640.346
650.326
660.222
670.535
680.0658
690.0142
70.938
700.475
710.723
720.173
730.251
740.0896
750.422
760.00765
770.0464
780.322
790.784
80.281
800.246
810.356
820.736
830.503
840.527
850.971
860.564
870.445
880.271
890.336
90.502
900.0238
910.721
920.32
930.513
940.0761
950.812
960.665
970.719
980.95
990.0176



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: CNhs11338


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)
0000149 (visual pigment cell)
0000255 (eukaryotic cell)
0000325 (stuff accumulating cell)
0000548 (animal cell)
0002371 (somatic cell)
0002586 (retinal 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)
0000073 (regional part of nervous system)
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)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000966 (retina)
0000970 (eye)
0001016 (nervous system)
0001032 (sensory system)
0001048 (primordium)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001781 (layer of retina)
0001782 (pigmented layer of retina)
0001802 (posterior segment of eyeball)
0002050 (embryonic structure)
0002104 (visual system)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0003056 (pre-chordal neural plate)
0003071 (eye primordium)
0003072 (optic cup)
0003075 (neural plate)
0004121 (ectoderm-derived structure)
0004128 (optic vesicle)
0004456 (entire sense organ system)
0004923 (organ component layer)
0005085 (ectodermal placode)
0005291 (embryonic tissue)
0005388 (photoreceptor array)
0005423 (developing anatomical structure)
0005424 (presumptive retinal pigmented epithelium)
0006598 (presumptive structure)
0007284 (presumptive neural plate)
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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