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FF:10031-101E4: 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:temporal lobe, 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
tissuetemporal lobe
dev stage32-61 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 number7090051
catalog numberCat:636564
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-Neural0.347
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-penis0.184
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-0.431
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0554
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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
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: CNhs10637

Jaspar motifP-value
MA0002.20.00871
MA0003.10.471
MA0004.10.523
MA0006.10.44
MA0007.10.228
MA0009.10.176
MA0014.10.577
MA0017.10.00699
MA0018.20.0405
MA0019.10.571
MA0024.10.805
MA0025.10.18
MA0027.10.549
MA0028.10.0464
MA0029.10.207
MA0030.10.168
MA0031.10.912
MA0035.20.207
MA0038.10.0518
MA0039.20.265
MA0040.10.383
MA0041.10.143
MA0042.10.63
MA0043.10.357
MA0046.10.394
MA0047.20.095
MA0048.10.0836
MA0050.10.00251
MA0051.10.0784
MA0052.10.0449
MA0055.10.0022
MA0057.10.918
MA0058.10.475
MA0059.10.0869
MA0060.10.178
MA0061.10.00787
MA0062.20.00877
MA0065.20.00141
MA0066.10.0389
MA0067.10.763
MA0068.10.139
MA0069.10.46
MA0070.10.0305
MA0071.10.0644
MA0072.10.603
MA0073.10.569
MA0074.10.241
MA0076.10.124
MA0077.10.175
MA0078.10.932
MA0079.20.274
MA0080.25.27052e-8
MA0081.10.0462
MA0083.10.244
MA0084.10.83
MA0087.10.401
MA0088.10.124
MA0090.10.296
MA0091.10.683
MA0092.10.461
MA0093.10.54
MA0099.21.96909e-9
MA0100.10.442
MA0101.10.00302
MA0102.20.148
MA0103.10.344
MA0104.20.402
MA0105.12.08375e-4
MA0106.10.0249
MA0107.10.00745
MA0108.20.0868
MA0111.10.36
MA0112.20.00115
MA0113.10.248
MA0114.10.00537
MA0115.10.544
MA0116.10.00288
MA0117.10.885
MA0119.10.0289
MA0122.10.815
MA0124.10.718
MA0125.10.208
MA0131.10.757
MA0135.10.00408
MA0136.11.10241e-9
MA0137.20.193
MA0138.20.108
MA0139.10.424
MA0140.10.0119
MA0141.10.0303
MA0142.10.97
MA0143.10.869
MA0144.10.196
MA0145.10.266
MA0146.10.0169
MA0147.10.288
MA0148.10.0851
MA0149.10.0141
MA0150.10.00136
MA0152.10.642
MA0153.10.545
MA0154.10.0513
MA0155.10.917
MA0156.16.9137e-6
MA0157.10.615
MA0159.10.00858
MA0160.10.0587
MA0162.10.127
MA0163.16.53645e-7
MA0164.10.819
MA0258.10.0154
MA0259.10.689



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: CNhs10637

Novel motifP-value
10.027
100.017
1000.273
1010.978
1020.663
1030.173
1040.194
1050.489
1060.0913
1070.148
1080.95
1090.0108
110.0159
1100.0373
1110.0517
1120.405
1130.76
1140.0725
1150.964
1160.236
1170.00724
1180.0939
1190.0985
120.835
1200.133
1210.751
1220.443
1230.344
1240.0803
1250.134
1260.0326
1270.567
1280.211
1290.574
139.20416e-4
1300.545
1310.091
1320.604
1330.00349
1340.256
1350.197
1360.00936
1370.674
1380.867
1390.0861
140.967
1400.117
1410.221
1420.963
1430.0121
1440.862
1450.105
1460.657
1470.861
1480.15
1490.451
150.06
1500.165
1510.701
1520.179
1530.528
1540.651
1550.343
1560.403
1570.376
1580.711
1590.164
160.0756
1600.243
1610.188
1620.902
1630.802
1640.0125
1650.0252
1660.776
1670.167
1680.716
1690.00775
170.217
180.239
190.245
20.9
200.0733
210.113
220.329
230.456
240.148
250.424
261.01354e-4
270.921
280.551
290.00632
30.0157
300.438
310.946
320.0463
330.0663
340.984
350.467
360.101
370.0356
380.323
390.294
40.95
400.0749
410.45
420.119
430.106
440.115
450.922
460.056
470.0552
480.053
490.123
50.376
500.375
510.561
520.735
530.934
540.511
550.278
560.512
570.238
580.25
590.229
60.524
600.0898
610.0656
620.141
630.178
640.228
650.363
660.268
670.3
680.245
690.569
70.0463
700.0252
710.00758
720.492
730.0508
740.43
750.0217
760.266
770.318
780.00179
790.321
80.0669
800.98
810.531
820.481
830.222
840.694
850.324
860.19
870.0177
880.851
890.681
90.641
900.018
910.331
920.407
930.827
940.0596
950.0301
960.955
970.799
980.18
990.949



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: CNhs10637


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
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
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)
0000955 (brain)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001871 (temporal lobe)
0001890 (forebrain)
0001893 (telencephalon)
0001950 (neocortex)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007135 (neural keel)
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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