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FF:10156-103A3: 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 17:15, 29 March 2012


Name:middle temporal gyrus, donor10252
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemedial temporal gyrus
dev stageNA
sexfemale
age76
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-Neural0.377
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-penis1.062
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-0.287
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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
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: CNhs12316

Jaspar motifP-value
MA0002.20.0456
MA0003.10.24
MA0004.10.384
MA0006.10.253
MA0007.10.322
MA0009.10.196
MA0014.10.639
MA0017.14.89648e-4
MA0018.20.512
MA0019.10.593
MA0024.10.92
MA0025.10.517
MA0027.10.545
MA0028.10.0565
MA0029.10.0371
MA0030.10.605
MA0031.10.999
MA0035.20.00737
MA0038.10.45
MA0039.20.139
MA0040.10.657
MA0041.10.398
MA0042.10.93
MA0043.11
MA0046.10.00189
MA0047.20.0598
MA0048.10.149
MA0050.10.0322
MA0051.10.0785
MA0052.10.522
MA0055.10.00122
MA0057.10.851
MA0058.10.311
MA0059.10.0733
MA0060.10.736
MA0061.10.00699
MA0062.20.00307
MA0065.21.39873e-4
MA0066.10.00913
MA0067.10.896
MA0068.10.512
MA0069.10.473
MA0070.10.589
MA0071.10.0118
MA0072.10.241
MA0073.10.436
MA0074.10.227
MA0076.10.104
MA0077.10.156
MA0078.10.88
MA0079.20.738
MA0080.27.78161e-8
MA0081.10.0337
MA0083.10.00922
MA0084.10.704
MA0087.10.868
MA0088.10.236
MA0090.10.369
MA0091.10.53
MA0092.10.27
MA0093.10.382
MA0099.22.93582e-20
MA0100.10.539
MA0101.10.00283
MA0102.20.186
MA0103.10.145
MA0104.20.416
MA0105.10.00179
MA0106.10.0472
MA0107.10.00319
MA0108.20.0928
MA0111.10.606
MA0112.20.00104
MA0113.10.534
MA0114.19.63936e-4
MA0115.10.321
MA0116.10.00864
MA0117.10.852
MA0119.10.12
MA0122.10.581
MA0124.10.671
MA0125.10.484
MA0131.10.996
MA0135.10.158
MA0136.17.06887e-12
MA0137.20.86
MA0138.20.467
MA0139.10.424
MA0140.10.00122
MA0141.10.00155
MA0142.10.762
MA0143.10.584
MA0144.10.428
MA0145.10.155
MA0146.10.0144
MA0147.10.309
MA0148.10.0823
MA0149.10.0245
MA0150.12.26098e-4
MA0152.10.478
MA0153.10.084
MA0154.10.0501
MA0155.10.48
MA0156.14.89123e-8
MA0157.10.658
MA0159.10.00402
MA0160.10.00821
MA0162.10.102
MA0163.12.25812e-5
MA0164.10.767
MA0258.10.00941
MA0259.10.828



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: CNhs12316

Novel motifP-value
10.0728
100.0602
1000.366
1010.469
1020.975
1030.139
1040.174
1050.157
1060.0464
1070.0983
1080.955
1090.00154
110.0126
1100.0516
1110.225
1120.376
1130.497
1140.186
1150.987
1160.125
1170.0123
1180.142
1190.213
120.479
1200.241
1210.26
1220.837
1230.58
1240.147
1250.192
1260.0238
1270.579
1280.145
1290.564
130.00113
1300.147
1310.0439
1320.558
1330.0843
1340.583
1350.188
1366.04582e-4
1370.861
1380.983
1390.115
140.829
1400.702
1410.579
1420.906
1430.107
1440.903
1450.137
1460.541
1470.832
1480.395
1490.243
150.093
1500.149
1510.657
1520.0747
1530.85
1540.458
1550.947
1560.466
1570.454
1580.137
1590.0153
160.0414
1600.217
1610.205
1620.66
1630.641
1640.0467
1650.045
1660.898
1670.993
1680.577
1690.0117
170.119
180.115
190.183
20.808
200.143
210.058
220.192
230.404
240.0224
250.475
263.8457e-4
270.74
280.644
290.00773
30.0523
300.931
310.861
320.0245
330.0488
340.598
350.636
360.194
370.0323
380.358
390.22
40.802
400.0272
410.312
420.259
430.13
440.156
450.633
460.0889
470.0684
480.0545
490.252
50.786
500.34
510.426
520.476
530.81
540.391
550.528
560.461
570.363
580.31
590.0723
60.904
600.0663
610.0735
620.187
630.212
640.207
650.256
660.164
670.357
680.21
690.371
70.0547
700.0558
710.0108
720.402
730.0231
740.941
750.0404
760.477
770.129
780.00223
790.394
80.0641
800.457
810.662
820.593
830.0485
840.593
850.244
860.221
875.25242e-5
880.796
890.356
90.337
900.086
910.863
920.532
930.94
940.202
950.00843
960.794
970.773
980.302
990.546



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: CNhs12316


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)
0000200 (gyrus)
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)
0002771 (middle temporal gyrus)
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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