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FF:10182-103D2: 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:locus coeruleus - 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
tissuelocus coeruleus
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-Neural0.217
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-penis0.691
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-0.337
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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: CNhs13808

Jaspar motifP-value
MA0002.20.0381
MA0003.10.229
MA0004.10.293
MA0006.10.477
MA0007.10.377
MA0009.10.192
MA0014.10.728
MA0017.10.00477
MA0018.20.0415
MA0019.10.803
MA0024.10.705
MA0025.10.698
MA0027.10.645
MA0028.10.0647
MA0029.10.205
MA0030.10.318
MA0031.10.78
MA0035.20.0112
MA0038.10.246
MA0039.20.341
MA0040.10.649
MA0041.10.81
MA0042.10.703
MA0043.10.499
MA0046.10.0208
MA0047.20.0854
MA0048.10.11
MA0050.10.0254
MA0051.10.123
MA0052.10.757
MA0055.10.00107
MA0057.10.748
MA0058.10.302
MA0059.10.075
MA0060.10.31
MA0061.10.00555
MA0062.20.00281
MA0065.20.00104
MA0066.10.0127
MA0067.10.573
MA0068.10.631
MA0069.10.732
MA0070.10.185
MA0071.10.0415
MA0072.10.714
MA0073.10.444
MA0074.10.182
MA0076.10.123
MA0077.10.0278
MA0078.10.839
MA0079.20.586
MA0080.24.87447e-8
MA0081.10.0273
MA0083.10.108
MA0084.10.227
MA0087.10.221
MA0088.10.13
MA0090.10.239
MA0091.10.333
MA0092.10.291
MA0093.10.344
MA0099.21.25751e-13
MA0100.10.699
MA0101.10.00462
MA0102.20.293
MA0103.10.068
MA0104.20.33
MA0105.11.5944e-4
MA0106.10.0258
MA0107.10.00405
MA0108.20.491
MA0111.10.5
MA0112.20.00104
MA0113.10.495
MA0114.10.00789
MA0115.10.829
MA0116.10.00233
MA0117.10.877
MA0119.10.1
MA0122.10.88
MA0124.10.862
MA0125.10.192
MA0131.10.819
MA0135.10.0141
MA0136.17.53915e-12
MA0137.20.0696
MA0138.20.252
MA0139.10.349
MA0140.10.00884
MA0141.10.0153
MA0142.10.356
MA0143.10.0631
MA0144.10.934
MA0145.10.347
MA0146.10.0212
MA0147.10.202
MA0148.10.0976
MA0149.10.0148
MA0150.10.0023
MA0152.10.742
MA0153.10.493
MA0154.10.0249
MA0155.10.654
MA0156.15.01237e-7
MA0157.10.583
MA0159.10.00991
MA0160.10.0724
MA0162.10.155
MA0163.11.00061e-7
MA0164.10.6
MA0258.10.0138
MA0259.10.646



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: CNhs13808

Novel motifP-value
10.0438
100.0425
1000.333
1010.824
1020.876
1030.0667
1040.139
1050.164
1060.0521
1070.167
1080.913
1090.00468
110.0105
1100.0334
1110.205
1120.419
1130.53
1140.133
1150.842
1160.156
1170.00714
1180.0982
1190.248
120.624
1200.141
1210.447
1220.915
1230.968
1240.134
1250.257
1260.0686
1270.45
1280.225
1290.448
130.00209
1300.226
1310.0231
1320.732
1330.0104
1340.69
1350.19
1360.00643
1370.574
1380.775
1390.108
140.898
1400.55
1410.496
1420.827
1430.0408
1440.875
1450.155
1460.396
1470.603
1480.297
1490.0955
150.0557
1500.159
1510.728
1520.167
1530.935
1540.455
1550.789
1560.229
1570.459
1580.145
1590.00649
160.0414
1600.196
1610.162
1620.84
1630.842
1640.0108
1650.114
1660.963
1670.783
1680.357
1690.0151
170.0898
180.072
190.285
20.895
200.171
210.0635
220.274
230.487
240.0379
250.53
261.51374e-4
270.722
280.791
290.00891
30.0371
300.866
310.901
320.0126
330.0704
340.739
350.378
360.173
370.0468
380.31
390.43
40.961
400.0577
410.29
420.209
430.118
440.122
450.714
460.0328
470.0488
480.0375
490.22
50.695
500.358
510.362
520.715
530.903
540.425
550.611
560.51
570.302
580.33
590.0664
60.939
600.114
610.0779
620.158
630.174
640.157
650.22
660.183
670.363
680.373
690.614
70.0847
700.0154
710.00566
720.356
730.0624
740.873
750.0204
760.303
770.162
780.00346
790.273
80.0575
800.458
810.427
820.621
830.0801
840.511
850.383
860.15
876.95285e-4
880.751
890.194
90.496
900.0842
910.699
920.562
930.585
940.129
950.0215
960.802
970.605
980.248
990.526



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: CNhs13808


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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