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FF:11215-116A9: 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 16:33, 29 March 2012


Name:Retinal Pigment Epithelial Cells, donor0
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueretina
dev stageNA
sexNA
ageNA
cell typeretinal pigment epithelial cell
cell lineNA
companySciencell
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog number6545
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-0.127
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-lymphoma0.443
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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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: CNhs10842

Jaspar motifP-value
MA0002.20.0446
MA0003.10.95
MA0004.10.0194
MA0006.10.278
MA0007.10.968
MA0009.10.942
MA0014.10.484
MA0017.10.625
MA0018.20.294
MA0019.10.103
MA0024.13.57349e-9
MA0025.10.323
MA0027.10.458
MA0028.10.885
MA0029.10.372
MA0030.10.0102
MA0031.10.0203
MA0035.20.467
MA0038.16.19709e-5
MA0039.20.027
MA0040.10.488
MA0041.10.852
MA0042.10.605
MA0043.10.187
MA0046.10.324
MA0047.20.0244
MA0048.10.547
MA0050.11.25041e-11
MA0051.11.25972e-5
MA0052.10.994
MA0055.10.00586
MA0057.10.467
MA0058.10.00696
MA0059.10.0702
MA0060.11.33316e-21
MA0061.13.42922e-6
MA0062.20.00229
MA0065.20.0535
MA0066.10.245
MA0067.10.329
MA0068.10.811
MA0069.10.411
MA0070.10.0923
MA0071.10.204
MA0072.10.459
MA0073.10.483
MA0074.10.985
MA0076.10.79
MA0077.10.0195
MA0078.10.89
MA0079.20.505
MA0080.21.14884e-12
MA0081.10.00246
MA0083.10.047
MA0084.10.04
MA0087.10.45
MA0088.10.218
MA0090.10.00558
MA0091.10.109
MA0092.10.733
MA0093.10.018
MA0099.20.906
MA0100.10.426
MA0101.12.89335e-4
MA0102.20.0079
MA0103.10.0336
MA0104.20.121
MA0105.11.081e-4
MA0106.10.406
MA0107.19.24164e-6
MA0108.23.92817e-5
MA0111.10.584
MA0112.20.281
MA0113.10.607
MA0114.10.0295
MA0115.10.165
MA0116.10.017
MA0117.10.267
MA0119.10.86
MA0122.10.239
MA0124.10.39
MA0125.10.0537
MA0131.10.388
MA0135.10.79
MA0136.14.50653e-10
MA0137.20.0229
MA0138.20.915
MA0139.10.198
MA0140.10.636
MA0141.10.0625
MA0142.10.989
MA0143.10.806
MA0144.10.00266
MA0145.10.303
MA0146.10.724
MA0147.10.379
MA0148.10.0376
MA0149.10.505
MA0150.10.0957
MA0152.10.94
MA0153.10.667
MA0154.10.238
MA0155.10.184
MA0156.12.33307e-10
MA0157.10.0782
MA0159.10.144
MA0160.10.204
MA0162.10.468
MA0163.10.0484
MA0164.10.202
MA0258.10.271
MA0259.10.625



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: CNhs10842

Novel motifP-value
10.285
100.00823
1000.266
1010.364
1020.419
1030.932
1040.63
1050.407
1060.00172
1070.435
1080.936
1090.369
110.851
1100.788
1110.0385
1120.00104
1130.0301
1140.0429
1150.88
1160.716
1170.0329
1180.575
1190.145
120.671
1200.635
1210.751
1220.447
1230.0709
1240.271
1250.893
1260.32
1270.933
1280.168
1290.604
130.485
1300.0101
1310.116
1320.975
1330.0729
1340.783
1350.0313
1360.143
1370.245
1382.62229e-4
1390.00773
140.571
1400.0287
1410.232
1420.734
1430.151
1440.249
1450.386
1460.902
1470.253
1480.111
1490.904
150.794
1500.48
1510.554
1520.997
1530.469
1540.38
1550.237
1560.35
1570.0557
1580.0996
1590.651
160.685
1600.894
1610.877
1620.253
1630.649
1640.0287
1650.0987
1660.321
1670.669
1680.238
1690.383
170.878
180.0523
190.419
20.476
200.709
210.416
220.605
230.0398
240.421
250.465
260.752
270.841
280.597
290.946
30.023
300.0744
310.748
320.007
330.405
340.601
350.262
360.904
370.411
380.84
390.848
40.863
400.0343
410.306
420.171
430.094
440.839
450.381
460.026
470.819
480.971
490.317
50.123
500.352
510.649
520.656
530.592
540.88
550.12
560.827
570.682
580.00305
590.345
60.765
600.012
610.888
620.00225
630.125
640.416
650.262
660.0252
670.958
680.77
690.0649
70.961
700.0757
710.0954
720.182
730.427
740.243
750.283
760.14
770.307
780.599
790.0306
80.707
800.157
810.209
820.0841
830.0389
840.921
850.0442
860.187
870.147
880.735
890.972
90.268
900.714
910.0219
920.0174
930.635
940.0768
950.374
960.45
970.975
980.103
990.0502



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: CNhs10842


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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