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FF:10036-101E9: 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 16:29, 29 March 2012


Name:occipital pole, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueoccipital pole
dev stage22-68 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3040374
catalog numberCat:636570
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-Neural0.294
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-penis0.0469
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-0.401
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.029
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs10643

Jaspar motifP-value
MA0002.20.00991
MA0003.10.455
MA0004.10.55
MA0006.10.451
MA0007.10.23
MA0009.10.161
MA0014.10.587
MA0017.10.00833
MA0018.20.038
MA0019.10.493
MA0024.10.886
MA0025.10.107
MA0027.10.732
MA0028.10.0791
MA0029.10.341
MA0030.10.0965
MA0031.10.796
MA0035.20.285
MA0038.10.0432
MA0039.20.266
MA0040.10.263
MA0041.10.137
MA0042.10.548
MA0043.10.246
MA0046.10.473
MA0047.20.191
MA0048.10.0881
MA0050.10.00335
MA0051.10.0983
MA0052.10.037
MA0055.10.00263
MA0057.10.962
MA0058.10.498
MA0059.10.0857
MA0060.10.116
MA0061.10.0109
MA0062.20.0205
MA0065.20.00108
MA0066.10.044
MA0067.10.777
MA0068.10.0898
MA0069.10.424
MA0070.10.0364
MA0071.10.0847
MA0072.10.736
MA0073.10.56
MA0074.10.252
MA0076.10.202
MA0077.10.204
MA0078.10.892
MA0079.20.29
MA0080.21.19425e-7
MA0081.10.0565
MA0083.10.221
MA0084.10.751
MA0087.10.411
MA0088.10.118
MA0090.10.292
MA0091.10.572
MA0092.10.434
MA0093.10.587
MA0099.27.89969e-8
MA0100.10.582
MA0101.10.00691
MA0102.20.178
MA0103.10.319
MA0104.20.411
MA0105.12.54738e-4
MA0106.10.0352
MA0107.10.0137
MA0108.20.0543
MA0111.10.374
MA0112.20.0013
MA0113.10.282
MA0114.10.00597
MA0115.10.393
MA0116.10.00229
MA0117.10.901
MA0119.10.024
MA0122.10.887
MA0124.10.716
MA0125.10.26
MA0131.10.81
MA0135.10.00676
MA0136.14.06492e-9
MA0137.20.393
MA0138.20.115
MA0139.10.416
MA0140.10.0386
MA0141.10.0419
MA0142.10.959
MA0143.10.9
MA0144.10.258
MA0145.10.288
MA0146.10.0137
MA0147.10.296
MA0148.10.151
MA0149.10.0148
MA0150.10.00331
MA0152.10.629
MA0153.10.579
MA0154.10.0448
MA0155.10.859
MA0156.14.48272e-5
MA0157.10.731
MA0159.10.00714
MA0160.10.0934
MA0162.10.132
MA0163.17.65644e-7
MA0164.10.798
MA0258.10.0149
MA0259.10.692



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: CNhs10643

Novel motifP-value
10.0234
100.0173
1000.248
1010.86
1020.757
1030.22
1040.244
1050.406
1060.0891
1070.137
1080.839
1090.016
110.0151
1100.0331
1110.0419
1120.358
1130.845
1140.0596
1150.892
1160.23
1170.00745
1180.0813
1190.0989
120.92
1200.132
1210.708
1220.391
1230.283
1240.066
1250.161
1260.0375
1270.499
1280.22
1290.666
130.00105
1300.752
1310.124
1320.67
1330.00594
1340.264
1350.193
1360.0154
1370.644
1380.771
1390.0686
140.91
1400.0831
1410.188
1420.803
1430.0106
1440.8
1450.0795
1460.75
1470.878
1480.116
1490.388
150.0661
1500.181
1510.705
1520.194
1530.539
1540.71
1550.316
1560.518
1570.45
1580.591
1590.366
160.0871
1600.215
1610.216
1620.971
1630.886
1640.0142
1650.0378
1660.836
1670.161
1680.68
1690.00692
170.215
180.238
190.249
20.899
200.0854
210.101
220.305
230.474
240.142
250.446
266.57634e-5
270.951
280.571
290.00849
30.0179
300.431
310.972
320.0394
330.0768
340.973
350.461
360.0842
370.0421
380.347
390.306
40.944
400.0741
410.492
420.14
430.108
440.0941
450.94
460.0481
470.0583
480.0561
490.119
50.376
500.436
510.55
520.747
530.998
540.506
550.295
560.507
570.212
580.25
590.22
60.475
600.0974
610.0613
620.136
630.179
640.223
650.347
660.385
670.346
680.336
690.462
70.0555
700.0263
710.00764
720.523
730.0573
740.49
750.0248
760.286
770.302
780.00261
790.22
80.0463
800.929
810.495
820.44
830.229
840.7
850.275
860.22
870.0291
880.864
890.604
90.642
900.0188
910.31
920.4
930.855
940.0554
950.0376
960.898
970.807
980.203
990.981



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: CNhs10643


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
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0001062 (anatomical entity)
0002902 (occipital pole)
0007023 (adult organism)

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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