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FF:10183-103D3: 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 17:39, 29 March 2012


Name:medial temporal gyrus - adult, donor10196
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
age60
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-Neural0.413
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-penis0.481
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.05
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.31
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.05
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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: CNhs13809

Jaspar motifP-value
MA0002.20.0115
MA0003.10.303
MA0004.10.239
MA0006.10.253
MA0007.10.225
MA0009.10.208
MA0014.10.574
MA0017.10.00426
MA0018.20.428
MA0019.10.848
MA0024.10.936
MA0025.10.841
MA0027.10.585
MA0028.10.0417
MA0029.10.0113
MA0030.10.567
MA0031.10.247
MA0035.20.00819
MA0038.10.745
MA0039.20.0312
MA0040.10.98
MA0041.10.502
MA0042.10.766
MA0043.10.406
MA0046.10.0012
MA0047.20.0173
MA0048.10.0996
MA0050.18.25096e-4
MA0051.10.0525
MA0052.10.167
MA0055.12.60387e-4
MA0057.10.842
MA0058.10.176
MA0059.10.104
MA0060.10.252
MA0061.10.00472
MA0062.24.80239e-4
MA0065.28.73925e-4
MA0066.10.0356
MA0067.10.748
MA0068.10.792
MA0069.10.482
MA0070.10.38
MA0071.10.0226
MA0072.10.215
MA0073.10.373
MA0074.10.304
MA0076.10.0791
MA0077.10.601
MA0078.10.903
MA0079.20.86
MA0080.23.61598e-9
MA0081.10.015
MA0083.10.00628
MA0084.10.897
MA0087.10.728
MA0088.10.148
MA0090.10.171
MA0091.10.689
MA0092.10.291
MA0093.10.239
MA0099.27.5924e-21
MA0100.10.473
MA0101.13.9208e-4
MA0102.20.0708
MA0103.10.366
MA0104.20.509
MA0105.10.00774
MA0106.10.0201
MA0107.18.18319e-4
MA0108.20.0391
MA0111.10.563
MA0112.20.0012
MA0113.10.357
MA0114.10.00224
MA0115.10.789
MA0116.10.0167
MA0117.10.989
MA0119.10.0421
MA0122.10.484
MA0124.10.3
MA0125.10.48
MA0131.10.756
MA0135.10.0247
MA0136.11.75475e-13
MA0137.20.604
MA0138.20.109
MA0139.10.55
MA0140.14.4387e-4
MA0141.10.0155
MA0142.10.968
MA0143.10.797
MA0144.10.406
MA0145.10.139
MA0146.10.00443
MA0147.10.408
MA0148.10.0169
MA0149.10.02
MA0150.15.19931e-5
MA0152.10.629
MA0153.10.0662
MA0154.10.0777
MA0155.10.631
MA0156.14.49125e-10
MA0157.10.298
MA0159.10.0126
MA0160.10.0103
MA0162.10.148
MA0163.15.10499e-4
MA0164.10.921
MA0258.10.00586
MA0259.10.913



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: CNhs13809

Novel motifP-value
10.096
100.0609
1000.3
1010.562
1020.837
1030.455
1040.103
1050.0279
1060.0519
1070.117
1080.712
1090.00341
110.0185
1100.0579
1110.336
1120.913
1130.937
1140.438
1150.196
1160.215
1170.0103
1180.149
1190.183
120.326
1200.513
1210.252
1220.806
1230.33
1240.0986
1250.223
1260.0388
1270.43
1280.205
1290.953
131.53987e-4
1300.089
1310.151
1320.802
1330.00894
1340.993
1350.171
1360.00228
1370.861
1380.701
1390.225
140.538
1400.549
1410.896
1420.712
1430.0644
1440.988
1450.113
1460.242
1470.49
1480.497
1490.581
150.0681
1500.157
1510.563
1520.0675
1530.767
1540.468
1550.688
1560.594
1570.351
1580.716
1590.162
160.149
1600.333
1610.179
1620.668
1630.912
1640.0475
1650.0648
1660.666
1670.903
1680.562
1690.00891
170.152
180.454
190.192
20.822
200.109
210.0801
220.171
230.415
240.0449
250.448
261.07106e-4
270.793
280.543
290.0252
30.0381
300.945
310.939
320.0815
330.0605
340.517
350.84
360.172
370.0406
380.289
390.256
40.723
400.0207
410.296
420.187
430.0976
440.996
450.579
460.171
470.125
480.0646
490.101
50.631
500.169
510.563
520.45
530.617
540.42
550.565
560.437
570.293
580.334
590.132
60.896
600.0528
610.0577
620.272
630.121
640.271
650.275
660.062
670.412
680.171
690.415
70.0272
700.152
710.0137
720.439
730.025
740.861
750.0419
760.391
770.154
780.0026
790.863
80.13
800.402
810.914
820.893
830.0071
840.374
850.287
860.221
870.00144
880.818
890.863
90.362
900.239
910.717
920.786
930.776
940.272
950.0149
960.985
970.582
980.303
990.676



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: CNhs13809


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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