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FF:10170-103B8: 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 17:38, 29 March 2012


Name:medial frontal 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 frontal 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-Neural0.443
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-penis0.804
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-0.328
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: CNhs13796

Jaspar motifP-value
MA0002.20.043
MA0003.10.327
MA0004.10.316
MA0006.10.211
MA0007.10.185
MA0009.10.253
MA0014.10.651
MA0017.10.00211
MA0018.20.0611
MA0019.10.516
MA0024.10.598
MA0025.10.551
MA0027.10.4
MA0028.10.0696
MA0029.10.0244
MA0030.10.75
MA0031.10.283
MA0035.20.0294
MA0038.10.629
MA0039.20.0407
MA0040.10.34
MA0041.10.663
MA0042.10.921
MA0043.10.704
MA0046.10.00219
MA0047.20.0101
MA0048.10.0798
MA0050.12.66735e-4
MA0051.10.0224
MA0052.10.723
MA0055.10.0012
MA0057.10.87
MA0058.10.216
MA0059.10.0991
MA0060.10.931
MA0061.10.00763
MA0062.20.00123
MA0065.27.05094e-4
MA0066.10.0429
MA0067.10.674
MA0068.10.696
MA0069.10.353
MA0070.10.543
MA0071.10.0179
MA0072.10.257
MA0073.10.314
MA0074.10.133
MA0076.10.122
MA0077.10.448
MA0078.10.997
MA0079.20.899
MA0080.27.36941e-10
MA0081.10.0249
MA0083.10.00566
MA0084.10.977
MA0087.10.829
MA0088.10.203
MA0090.10.301
MA0091.10.413
MA0092.10.348
MA0093.10.316
MA0099.21.17885e-19
MA0100.10.59
MA0101.10.00134
MA0102.20.113
MA0103.10.359
MA0104.20.611
MA0105.10.0129
MA0106.10.0424
MA0107.10.00251
MA0108.20.249
MA0111.10.571
MA0112.20.00244
MA0113.10.481
MA0114.10.00215
MA0115.10.852
MA0116.10.0188
MA0117.10.88
MA0119.10.0726
MA0122.10.511
MA0124.10.832
MA0125.10.455
MA0131.10.882
MA0135.10.0492
MA0136.17.11915e-14
MA0137.20.64
MA0138.20.0784
MA0139.10.432
MA0140.10.00564
MA0141.10.0112
MA0142.10.76
MA0143.10.653
MA0144.10.295
MA0145.10.134
MA0146.10.00457
MA0147.10.458
MA0148.10.0219
MA0149.10.0459
MA0150.15.74107e-4
MA0152.10.516
MA0153.10.0552
MA0154.10.068
MA0155.10.516
MA0156.13.86465e-10
MA0157.10.231
MA0159.10.00808
MA0160.10.0155
MA0162.10.142
MA0163.13.28718e-4
MA0164.10.946
MA0258.10.0153
MA0259.10.95



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: CNhs13796

Novel motifP-value
10.0852
100.0581
1000.329
1010.483
1020.839
1030.352
1040.109
1050.0509
1060.0277
1070.0626
1080.997
1090.00288
110.0195
1100.054
1110.35
1120.653
1130.438
1140.387
1150.999
1160.091
1170.00835
1180.123
1190.273
120.41
1200.313
1210.167
1220.981
1230.619
1240.00699
1250.428
1260.0105
1270.588
1280.218
1290.595
133.05299e-4
1300.0537
1310.105
1320.839
1330.00315
1340.67
1350.164
1364.88254e-4
1370.711
1380.779
1390.164
140.744
1400.47
1410.94
1420.666
1430.0982
1440.917
1450.0814
1460.244
1470.451
1480.448
1490.221
150.116
1500.122
1510.634
1520.0589
1530.896
1540.442
1550.766
1560.309
1570.425
1580.384
1590.0727
160.0594
1600.268
1610.156
1620.657
1630.687
1640.0168
1650.031
1660.935
1670.821
1680.352
1690.0125
170.154
180.23
190.161
20.688
200.101
210.0863
220.139
230.442
240.0319
250.506
263.10475e-5
270.956
280.619
290.0147
30.0493
300.967
310.895
320.0314
330.0566
340.458
350.871
360.265
370.0468
380.347
390.156
40.99
400.0353
410.393
420.25
430.0992
440.302
450.579
460.105
470.0867
480.044
490.214
50.71
500.149
510.501
520.354
530.929
540.406
550.392
560.498
570.449
580.423
590.0528
60.828
600.0456
610.0323
620.293
630.104
640.364
650.305
660.14
670.374
680.233
690.388
70.0388
700.0616
710.00984
720.389
730.022
740.883
750.0401
760.519
770.136
780.00159
790.253
80.0928
800.492
810.952
820.901
830.0319
840.557
850.368
860.187
871.72279e-4
880.878
890.794
90.287
900.411
910.825
920.809
930.746
940.246
950.0131
960.87
970.577
980.379
990.598



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: CNhs13796


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

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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