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FF:10150-102I6: 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 17:14, 29 March 2012


Name:medial temporal gyrus, adult, 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 frontal 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-Neural0.376
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-penis0.951
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-0.295
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.097
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: CNhs12310

Jaspar motifP-value
MA0002.20.0243
MA0003.10.254
MA0004.10.374
MA0006.10.274
MA0007.10.284
MA0009.10.14
MA0014.10.647
MA0017.16.33837e-4
MA0018.20.459
MA0019.10.64
MA0024.10.897
MA0025.10.356
MA0027.10.544
MA0028.10.0574
MA0029.10.0207
MA0030.10.55
MA0031.10.954
MA0035.20.00457
MA0038.10.366
MA0039.20.142
MA0040.10.793
MA0041.10.513
MA0042.10.961
MA0043.10.97
MA0046.10.00197
MA0047.20.0353
MA0048.10.136
MA0050.10.0382
MA0051.10.0907
MA0052.10.925
MA0055.19.97132e-4
MA0057.10.851
MA0058.10.316
MA0059.10.0704
MA0060.10.713
MA0061.10.00716
MA0062.20.00235
MA0065.21.62703e-4
MA0066.10.00903
MA0067.10.94
MA0068.10.885
MA0069.10.526
MA0070.10.493
MA0071.10.0166
MA0072.10.265
MA0073.10.379
MA0074.10.205
MA0076.10.0949
MA0077.10.251
MA0078.10.7
MA0079.20.631
MA0080.27.23011e-8
MA0081.10.0345
MA0083.10.00751
MA0084.10.761
MA0087.10.755
MA0088.10.194
MA0090.10.369
MA0091.10.477
MA0092.10.28
MA0093.10.386
MA0099.25.10555e-19
MA0100.10.569
MA0101.10.00283
MA0102.20.221
MA0103.10.145
MA0104.20.42
MA0105.10.00158
MA0106.10.0368
MA0107.10.00452
MA0108.20.162
MA0111.10.559
MA0112.29.35553e-4
MA0113.10.407
MA0114.19.78659e-4
MA0115.10.29
MA0116.10.00882
MA0117.10.907
MA0119.10.104
MA0122.10.513
MA0124.10.703
MA0125.10.421
MA0131.10.997
MA0135.10.127
MA0136.16.64524e-12
MA0137.20.626
MA0138.20.347
MA0139.10.425
MA0140.18.54422e-4
MA0141.10.00255
MA0142.10.808
MA0143.10.83
MA0144.10.57
MA0145.10.16
MA0146.10.0122
MA0147.10.298
MA0148.10.0547
MA0149.10.0236
MA0150.13.50726e-4
MA0152.10.496
MA0153.10.0507
MA0154.10.0522
MA0155.10.517
MA0156.11.28055e-7
MA0157.10.649
MA0159.10.00478
MA0160.10.00827
MA0162.10.106
MA0163.12.05321e-5
MA0164.10.771
MA0258.10.00793
MA0259.10.818



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: CNhs12310

Novel motifP-value
10.0633
100.0542
1000.293
1010.45
1020.866
1030.117
1040.144
1050.113
1060.0536
1070.106
1080.974
1090.00251
110.0142
1100.0498
1110.161
1120.413
1130.556
1140.157
1150.885
1160.163
1170.011
1180.12
1190.173
120.503
1200.221
1210.332
1220.914
1230.597
1240.114
1250.164
1260.0153
1270.554
1280.171
1290.524
139.39575e-4
1300.226
1310.0686
1320.598
1330.0499
1340.613
1350.225
1360.00179
1370.943
1380.964
1390.114
140.793
1400.41
1410.612
1420.763
1430.0489
1440.869
1450.123
1460.484
1470.769
1480.303
1490.227
150.0878
1500.165
1510.639
1520.0904
1530.835
1540.479
1550.877
1560.432
1570.452
1580.364
1590.0316
160.0461
1600.247
1610.223
1620.684
1630.707
1640.0423
1650.0399
1660.932
1670.815
1680.556
1690.00944
170.134
180.127
190.185
20.891
200.127
210.0605
220.189
230.448
240.0414
250.457
261.85883e-4
270.81
280.653
290.00722
30.0494
300.962
310.888
320.0266
330.0495
340.635
350.621
360.162
370.0367
380.349
390.25
40.692
400.0281
410.293
420.245
430.12
440.168
450.682
460.0747
470.0679
480.057
490.21
50.59
500.332
510.434
520.531
530.85
540.397
550.561
560.484
570.313
580.309
590.0844
60.946
600.0803
610.0667
620.196
630.185
640.21
650.282
660.15
670.363
680.126
690.292
70.0515
700.0537
710.011
720.414
730.0299
740.922
750.0422
760.434
770.148
780.00223
790.359
80.0604
800.527
810.705
820.625
830.0663
840.671
850.248
860.237
872.09946e-4
880.795
890.392
90.37
900.0724
910.751
920.526
930.997
940.191
950.0133
960.797
970.703
980.234
990.595



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: CNhs12310


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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