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FF:10000-101A1: 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 15:17, 29 March 2012


Name:Clontech Human Universal Reference Total RNA, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageUNDEFINED
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 number9052727A
catalog numberCat:636538
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-caudate0.509
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0.101
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-penis0.0837
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-0.0549
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
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-Whole0.0275
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0.123
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0.0535
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: CNhs10608

Jaspar motifP-value
MA0002.20.00415
MA0003.10.402
MA0004.10.679
MA0006.10.966
MA0007.10.571
MA0009.10.399
MA0014.10.969
MA0017.10.31
MA0018.21.7605e-4
MA0019.10.0335
MA0024.10.391
MA0025.10.314
MA0027.10.478
MA0028.10.157
MA0029.10.2
MA0030.10.0609
MA0031.10.257
MA0035.20.145
MA0038.14.76826e-4
MA0039.20.18
MA0040.10.67
MA0041.10.0419
MA0042.10.552
MA0043.10.02
MA0046.11.96936e-16
MA0047.20.766
MA0048.10.0848
MA0050.10.338
MA0051.10.412
MA0052.10.235
MA0055.10.132
MA0057.10.746
MA0058.10.696
MA0059.10.0527
MA0060.11.19791e-22
MA0061.11.19177e-4
MA0062.20.0923
MA0065.20.434
MA0066.10.144
MA0067.10.968
MA0068.10.133
MA0069.10.859
MA0070.10.0987
MA0071.10.207
MA0072.10.722
MA0073.10.924
MA0074.10.413
MA0076.10.482
MA0077.10.155
MA0078.10.225
MA0079.20.0646
MA0080.24.33936e-4
MA0081.10.0587
MA0083.10.0745
MA0084.10.617
MA0087.10.209
MA0088.10.117
MA0090.10.946
MA0091.10.472
MA0092.10.221
MA0093.10.728
MA0099.21.3414e-11
MA0100.14.94038e-6
MA0101.19.07143e-4
MA0102.20.39
MA0103.10.955
MA0104.20.434
MA0105.12.62672e-10
MA0106.10.00174
MA0107.11.05621e-4
MA0108.29.88331e-13
MA0111.10.218
MA0112.20.00159
MA0113.10.248
MA0114.10.742
MA0115.10.0323
MA0116.14.50203e-4
MA0117.10.481
MA0119.10.0113
MA0122.10.54
MA0124.10.484
MA0125.10.249
MA0131.10.607
MA0135.10.00717
MA0136.10.00447
MA0137.20.761
MA0138.20.365
MA0139.10.472
MA0140.10.157
MA0141.10.415
MA0142.10.732
MA0143.10.189
MA0144.10.379
MA0145.10.914
MA0146.10.333
MA0147.10.233
MA0148.10.497
MA0149.10.00403
MA0150.16.68994e-5
MA0152.10.719
MA0153.13.48591e-12
MA0154.10.00162
MA0155.10.613
MA0156.10.0166
MA0157.10.378
MA0159.10.193
MA0160.10.995
MA0162.10.399
MA0163.12.18127e-8
MA0164.10.609
MA0258.10.0476
MA0259.10.63



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: CNhs10608

Novel motifP-value
10.0125
100.00968
1000.702
1010.759
1020.932
1030.231
1040.518
1050.821
1060.00676
1070.164
1080.426
1090.144
110.0314
1100.0733
1110.0294
1120.072
1130.912
1140.0263
1150.971
1160.251
1170.022
1180.0634
1190.125
120.99
1200.0141
1210.52
1220.544
1230.103
1240.0961
1250.121
1260.975
1270.318
1280.0407
1290.738
130.0594
1300.254
1310.911
1320.476
1330.199
1340.251
1350.94
1360.941
1370.148
1380.27
1390.134
140.844
1400.0234
1410.0488
1420.796
1430.291
1440.721
1450.157
1460.771
1470.554
1480.0418
1490.435
150.163
1500.138
1510.457
1520.316
1530.48
1540.507
1550.897
1560.774
1570.773
1580.568
1590.858
160.226
1600.0588
1610.716
1620.824
1630.375
1641.28513e-4
1650.422
1660.692
1670.0197
1680.987
1690.0583
170.268
180.0362
190.765
20.873
200.239
210.228
220.626
230.246
240.918
250.542
260.0158
270.646
280.838
290.0254
30.0166
300.066
310.52
320.104
330.373
340.562
350.162
360.0192
370.0222
380.607
390.98
40.233
400.369
410.497
420.135
430.112
440.299
450.56
460.0268
470.152
480.15
490.434
50.196
500.992
510.373
520.938
530.793
540.426
550.156
560.383
570.075
580.5
590.227
60.463
600.091
610.437
620.151
630.179
640.324
650.385
665.91442e-5
670.294
680.443
690.992
70.239
700.0497
710.0139
720.647
730.0804
740.239
750.0106
760.044
770.565
780.00639
790.221
80.17
800.408
810.216
820.301
830.568
840.548
850.103
860.173
870.985
880.76
890.444
90.919
900.0183
910.168
920.193
930.462
940.00764
950.189
960.585
970.889
980.268
990.904



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: CNhs10608


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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