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FF:10030-101E3: 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 16:28, 29 March 2012


Name:retina, adult, pool1
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 stage24-65 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number9100123A
catalog numberCat:636579
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-Neural0.058
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-penis0.0158
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-lymphoma-0.337
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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-Whole0.03
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: CNhs10636

Jaspar motifP-value
MA0002.20.00322
MA0003.10.852
MA0004.10.257
MA0006.10.893
MA0007.10.39
MA0009.10.366
MA0014.10.428
MA0017.10.119
MA0018.20.264
MA0019.10.324
MA0024.10.318
MA0025.10.0467
MA0027.10.708
MA0028.10.0272
MA0029.10.317
MA0030.10.0149
MA0031.10.608
MA0035.20.57
MA0038.10.0142
MA0039.20.837
MA0040.10.452
MA0041.10.211
MA0042.10.374
MA0043.10.988
MA0046.10.66
MA0047.20.422
MA0048.10.202
MA0050.10.802
MA0051.10.828
MA0052.11.26616e-4
MA0055.10.0183
MA0057.10.949
MA0058.10.298
MA0059.10.00786
MA0060.10.266
MA0061.10.00148
MA0062.20.00174
MA0065.20.00532
MA0066.10.0333
MA0067.10.957
MA0068.10.00327
MA0069.10.82
MA0070.10.955
MA0071.10.569
MA0072.10.215
MA0073.10.509
MA0074.10.597
MA0076.10.0577
MA0077.10.94
MA0078.10.309
MA0079.20.176
MA0080.24.54184e-4
MA0081.10.156
MA0083.10.545
MA0084.10.641
MA0087.10.338
MA0088.10.0873
MA0090.10.632
MA0091.10.741
MA0092.10.53
MA0093.10.297
MA0099.23.33504e-13
MA0100.10.211
MA0101.10.00651
MA0102.20.272
MA0103.10.245
MA0104.20.0558
MA0105.15.94374e-8
MA0106.10.00297
MA0107.10.00597
MA0108.23.21087e-9
MA0111.10.377
MA0112.20.00276
MA0113.10.575
MA0114.10.0404
MA0115.10.164
MA0116.17.80428e-4
MA0117.10.426
MA0119.10.102
MA0122.10.393
MA0124.10.743
MA0125.10.00548
MA0131.10.91
MA0135.10.00575
MA0136.17.65245e-5
MA0137.20.911
MA0138.20.286
MA0139.10.422
MA0140.10.288
MA0141.10.0861
MA0142.10.378
MA0143.10.899
MA0144.10.297
MA0145.10.691
MA0146.10.126
MA0147.10.0162
MA0148.10.165
MA0149.10.0113
MA0150.14.976e-4
MA0152.10.866
MA0153.10.591
MA0154.10.0227
MA0155.10.872
MA0156.16.85219e-4
MA0157.10.581
MA0159.10.104
MA0160.10.161
MA0162.10.266
MA0163.18.99711e-11
MA0164.10.283
MA0258.10.046
MA0259.10.178



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: CNhs10636

Novel motifP-value
10.0139
100.0115
1000.196
1010.978
1020.891
1030.0214
1040.628
1050.858
1060.212
1070.491
1080.652
1090.0267
110.0245
1100.0532
1116.98903e-4
1120.39
1130.254
1140.0305
1150.686
1160.376
1170.00536
1180.025
1190.248
120.924
1200.0628
1210.926
1220.577
1230.0804
1240.761
1250.084
1260.193
1270.418
1280.52
1290.195
130.0233
1300.464
1310.114
1320.442
1330.0176
1340.136
1350.971
1360.0723
1370.931
1380.213
1390.106
140.71
1400.425
1410.0429
1420.98
1430.00822
1440.694
1450.294
1460.679
1470.673
1480.0173
1490.997
150.0201
1500.177
1510.71
1520.406
1530.964
1540.501
1550.179
1560.508
1570.301
1580.582
1590.386
160.052
1600.132
1610.353
1620.849
1630.761
1640.00845
1650.167
1660.428
1670.0141
1680.94
1690.0119
170.198
180.0517
190.669
20.593
200.103
210.0886
220.655
230.863
240.396
250.273
260.0038
270.934
280.845
290.00628
30.0462
300.162
310.832
320.0273
330.0453
340.44
350.403
360.0323
370.0686
380.478
390.878
40.694
400.159
410.183
420.168
430.111
440.187
450.686
460.0409
470.0439
480.0807
490.0965
50.266
500.972
510.5
520.776
530.806
540.659
550.534
560.628
570.122
580.395
590.326
60.57
600.285
610.0474
620.169
630.283
640.186
650.57
660.125
670.449
680.257
690.359
70.169
700.00813
710.00869
720.495
730.0816
740.449
750.00484
760.135
770.902
780.0492
790.244
80.0354
800.23
810.247
820.504
830.778
840.644
850.533
860.289
870.0153
880.726
890.238
90.722
900.0299
910.472
920.384
930.676
940.0545
950.0553
960.239
970.921
980.0973
990.921



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: CNhs10636


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

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)
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)
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)
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)
0005085 (ectodermal placode)
0005291 (embryonic tissue)
0005388 (photoreceptor array)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
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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