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FF:10016-101C7: 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 16:26, 29 March 2012


Name:heart, 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
tissueheart
dev stage70,73,74 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -7
catalog numberCat:AM6000 Lot:0910061 -7
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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
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-penis0.0352
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-0.437
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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: CNhs10621

Jaspar motifP-value
MA0002.20.0928
MA0003.10.128
MA0004.10.0616
MA0006.10.193
MA0007.10.273
MA0009.10.0313
MA0014.10.958
MA0017.10.209
MA0018.20.279
MA0019.10.131
MA0024.10.00477
MA0025.10.792
MA0027.10.92
MA0028.11.3126e-7
MA0029.10.0694
MA0030.10.428
MA0031.10.197
MA0035.21.67097e-5
MA0038.10.1
MA0039.20.978
MA0040.10.773
MA0041.10.00966
MA0042.10.222
MA0043.10.153
MA0046.10.264
MA0047.20.605
MA0048.10.00853
MA0050.10.0205
MA0051.10.615
MA0052.11.25486e-48
MA0055.10.00359
MA0057.10.713
MA0058.10.0153
MA0059.10.0043
MA0060.10.0391
MA0061.13.57798e-4
MA0062.23.42014e-12
MA0065.20.665
MA0066.10.721
MA0067.10.638
MA0068.10.00277
MA0069.10.636
MA0070.10.856
MA0071.10.0591
MA0072.10.74
MA0073.10.884
MA0074.10.875
MA0076.14.45146e-10
MA0077.10.285
MA0078.10.6
MA0079.20.0514
MA0080.20.00197
MA0081.10.13
MA0083.11.58478e-5
MA0084.10.925
MA0087.10.468
MA0088.10.00504
MA0090.10.00291
MA0091.10.117
MA0092.10.0491
MA0093.10.0431
MA0099.23.04753e-9
MA0100.10.0319
MA0101.10.0528
MA0102.20.443
MA0103.10.116
MA0104.22.87239e-4
MA0105.19.88699e-6
MA0106.10.159
MA0107.10.0272
MA0108.24.05517e-19
MA0111.10.999
MA0112.20.404
MA0113.10.00273
MA0114.10.807
MA0115.10.219
MA0116.10.00431
MA0117.10.461
MA0119.10.597
MA0122.10.0341
MA0124.10.334
MA0125.10.837
MA0131.10.0436
MA0135.10.587
MA0136.13.4664e-7
MA0137.20.177
MA0138.20.485
MA0139.10.0617
MA0140.10.0182
MA0141.12.08354e-5
MA0142.10.0726
MA0143.10.4
MA0144.10.58
MA0145.10.094
MA0146.10.543
MA0147.11.10722e-4
MA0148.10.433
MA0149.10.448
MA0150.10.0775
MA0152.10.458
MA0153.10.644
MA0154.10.86
MA0155.10.312
MA0156.11.00887e-7
MA0157.10.462
MA0159.10.452
MA0160.12.48134e-5
MA0162.10.998
MA0163.11.03907e-7
MA0164.10.315
MA0258.10.156
MA0259.10.0412



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: CNhs10621

Novel motifP-value
10.49
100.0285
1000.617
1010.887
1020.826
1030.113
1040.474
1050.158
1060.548
1070.146
1080.542
1090.418
110.496
1100.108
1110.138
1120.45
1130.796
1140.553
1150.722
1160.445
1170.0174
1180.0158
1190.322
120.877
1200.00514
1210.904
1220.708
1230.00596
1240.844
1250.578
1260.789
1270.6
1280.263
1290.43
130.117
1300.339
1310.0131
1320.168
1330.19
1340.0139
1350.129
1360.63
1370.979
1380.994
1390.489
140.454
1400.861
1410.983
1420.994
1430.153
1440.946
1450.767
1460.207
1470.0493
1480.529
1490.407
150.854
1500.835
1510.418
1520.204
1530.37
1540.673
1550.238
1560.229
1570.848
1580.228
1590.332
160.455
1600.802
1610.339
1620.736
1630.507
1640.00587
1650.775
1660.0397
1670.0587
1680.259
1690.977
170.836
180.495
190.277
20.218
200.0453
210.279
220.205
230.0688
240.0929
250.608
260.0308
270.956
280.674
290.00239
30.229
300.0894
310.847
320.442
330.286
340.0559
350.674
360.0894
370.372
380.839
390.125
40.668
400.0664
410.679
420.279
430.848
440.571
450.132
460.389
470.16
480.133
490.978
50.716
500.709
510.676
520.0548
530.911
540.524
550.233
560.791
570.237
580.648
590.609
60.714
600.322
610.0697
620.958
630.905
640.479
650.303
660.017
670.19
680.878
690.757
70.856
700.164
710.0105
720.938
730.681
740.0661
750.0171
760.0783
770.208
780.789
790.856
80.676
800.165
810.699
820.806
830.614
840.897
850.0433
860.754
870.263
880.777
890.276
90.376
900.0776
910.131
920.615
930.61
940.0502
950.0335
960.806
970.381
980.17
990.0921



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: CNhs10621


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)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0007023 (adult organism)
0007100 (primary circulatory organ)

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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