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FF:10084-102B3: 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 16:54, 29 March 2012


Name:brain, adult, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stage18 years old adult
sexmale
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 number8101369A-4
catalog numberCat: 636643 Lot: 8101369A-4
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-Neural0.294
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-penis0.647
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-0.449
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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
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: CNhs11796

Jaspar motifP-value
MA0002.20.00513
MA0003.10.48
MA0004.10.451
MA0006.10.533
MA0007.10.323
MA0009.10.154
MA0014.10.485
MA0017.10.0563
MA0018.20.0515
MA0019.10.944
MA0024.10.735
MA0025.10.252
MA0027.10.617
MA0028.10.0146
MA0029.10.143
MA0030.10.117
MA0031.10.97
MA0035.20.188
MA0038.10.158
MA0039.20.14
MA0040.10.315
MA0041.10.608
MA0042.10.854
MA0043.10.566
MA0046.10.141
MA0047.20.338
MA0048.10.0919
MA0050.16.34201e-5
MA0051.10.0271
MA0052.10.207
MA0055.10.00103
MA0057.10.929
MA0058.10.364
MA0059.10.0772
MA0060.10.577
MA0061.10.00316
MA0062.25.14582e-4
MA0065.20.00785
MA0066.10.045
MA0067.10.779
MA0068.10.113
MA0069.10.454
MA0070.10.025
MA0071.10.11
MA0072.10.602
MA0073.10.563
MA0074.10.355
MA0076.10.0197
MA0077.10.188
MA0078.10.977
MA0079.20.311
MA0080.27.82445e-9
MA0081.10.0135
MA0083.10.154
MA0084.10.291
MA0087.10.545
MA0088.10.133
MA0090.10.289
MA0091.10.597
MA0092.10.383
MA0093.10.455
MA0099.21.93854e-16
MA0100.10.135
MA0101.11.96213e-4
MA0102.20.0215
MA0103.10.404
MA0104.20.404
MA0105.11.18176e-4
MA0106.10.0194
MA0107.18.80354e-4
MA0108.20.215
MA0111.10.454
MA0112.20.00219
MA0113.10.465
MA0114.10.0444
MA0115.10.846
MA0116.10.00243
MA0117.10.895
MA0119.10.0667
MA0122.10.473
MA0124.10.848
MA0125.10.173
MA0131.10.608
MA0135.17.78804e-4
MA0136.13.9914e-13
MA0137.20.177
MA0138.20.0248
MA0139.10.479
MA0140.10.0107
MA0141.10.153
MA0142.10.704
MA0143.10.657
MA0144.10.323
MA0145.10.265
MA0146.10.0248
MA0147.10.278
MA0148.10.235
MA0149.10.0112
MA0150.16.85372e-5
MA0152.10.561
MA0153.10.157
MA0154.10.0368
MA0155.10.935
MA0156.12.19081e-9
MA0157.10.633
MA0159.10.0256
MA0160.10.0968
MA0162.10.172
MA0163.11.36054e-6
MA0164.10.858
MA0258.10.0579
MA0259.10.602



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: CNhs11796

Novel motifP-value
10.0371
100.0171
1000.35
1010.866
1020.669
1030.0894
1040.173
1050.356
1060.148
1070.192
1080.887
1090.00905
110.0223
1100.0273
1110.158
1120.443
1130.535
1140.106
1150.654
1160.382
1170.00522
1180.107
1190.405
120.719
1200.139
1210.612
1220.509
1230.854
1240.0284
1250.325
1260.0163
1270.371
1280.391
1290.881
134.29961e-4
1300.282
1310.155
1320.316
1330.00461
1340.605
1350.265
1360.00794
1370.359
1380.821
1390.17
140.93
1400.375
1410.302
1420.898
1430.0086
1440.964
1450.12
1460.386
1470.851
1480.187
1490.736
150.0475
1500.136
1510.767
1520.227
1530.499
1540.499
1550.483
1560.893
1570.264
1580.395
1590.435
160.0675
1600.269
1610.188
1620.889
1630.738
1640.0155
1650.0534
1660.988
1670.344
1680.631
1690.0131
170.192
180.168
190.343
20.777
200.0709
210.0781
220.316
230.503
240.05
250.311
265.47113e-5
270.924
280.551
290.00338
30.0106
300.512
310.926
320.079
330.0473
340.962
350.565
360.121
370.0441
380.364
390.309
40.914
400.095
410.313
420.0937
430.0968
440.471
450.895
460.069
470.0878
480.0606
490.183
50.361
500.325
510.531
520.878
530.67
540.567
550.444
560.54
570.231
580.293
590.245
60.524
600.0993
610.0443
620.164
630.225
640.247
650.443
660.115
670.297
680.583
690.689
70.0267
700.0355
710.00431
720.299
730.0621
740.517
750.0201
760.244
770.432
780.00174
790.457
80.0964
800.611
810.578
820.566
830.0681
840.744
850.542
860.172
870.0191
880.892
890.63
90.461
900.0207
910.391
920.555
930.841
940.05
950.0212
960.942
970.73
980.316
990.941



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: CNhs11796


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
0000033 (head)
0000061 (anatomical structure)
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)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)
0007023 (adult organism)

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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