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FF:10050-101G5: 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 16:51, 29 March 2012


Name:heart, adult, diseased post-infarction, donor1
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 stage92 years old adult
sexfemale
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 number9070074A
catalog numberCat:636582
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
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-penis0.655
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-lymphoma0.0845
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs11757

Jaspar motifP-value
MA0002.28.77945e-6
MA0003.10.224
MA0004.10.0203
MA0006.10.121
MA0007.10.333
MA0009.10.49
MA0014.10.442
MA0017.10.533
MA0018.20.364
MA0019.10.289
MA0024.10.835
MA0025.10.303
MA0027.10.378
MA0028.11.98193e-7
MA0029.10.195
MA0030.10.517
MA0031.10.483
MA0035.20.00266
MA0038.10.14
MA0039.20.128
MA0040.10.047
MA0041.10.915
MA0042.10.978
MA0043.10.0055
MA0046.10.857
MA0047.20.278
MA0048.10.0201
MA0050.11.29147e-4
MA0051.10.00711
MA0052.13.75547e-29
MA0055.10.383
MA0057.10.374
MA0058.10.00384
MA0059.10.00123
MA0060.10.947
MA0061.13.45108e-9
MA0062.22.30756e-15
MA0065.20.126
MA0066.10.851
MA0067.10.0757
MA0068.10.19
MA0069.10.993
MA0070.10.329
MA0071.10.0248
MA0072.11
MA0073.10.98
MA0074.10.611
MA0076.11.45721e-10
MA0077.10.306
MA0078.10.57
MA0079.20.0762
MA0080.22.51351e-9
MA0081.10.00176
MA0083.10.00654
MA0084.10.508
MA0087.10.719
MA0088.10.0359
MA0090.12.25699e-4
MA0091.10.731
MA0092.10.497
MA0093.10.0177
MA0099.24.74007e-15
MA0100.10.0151
MA0101.13.75303e-5
MA0102.20.0169
MA0103.12.98116e-4
MA0104.21.46415e-4
MA0105.11.51072e-8
MA0106.10.188
MA0107.12.97469e-6
MA0108.23.66855e-22
MA0111.10.828
MA0112.20.216
MA0113.10.00234
MA0114.10.288
MA0115.10.00578
MA0116.10.00289
MA0117.10.119
MA0119.10.56
MA0122.10.223
MA0124.10.827
MA0125.10.942
MA0131.10.188
MA0135.10.0952
MA0136.11.25488e-13
MA0137.20.0741
MA0138.20.268
MA0139.10.431
MA0140.10.426
MA0141.11.69005e-5
MA0142.10.00946
MA0143.10.073
MA0144.10.085
MA0145.10.0527
MA0146.10.128
MA0147.12.00207e-4
MA0148.10.926
MA0149.10.99
MA0150.14.78133e-4
MA0152.10.865
MA0153.10.743
MA0154.10.22
MA0155.10.293
MA0156.15.73633e-14
MA0157.10.11
MA0159.10.123
MA0160.10.00269
MA0162.10.529
MA0163.11.20171e-4
MA0164.10.725
MA0258.10.0502
MA0259.10.0726



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: CNhs11757

Novel motifP-value
10.549
100.0439
1000.63
1010.963
1020.382
1030.158
1040.466
1050.357
1060.801
1070.0825
1080.198
1090.905
110.571
1100.398
1110.366
1120.92
1130.741
1140.15
1150.24
1160.76
1170.0266
1180.0723
1190.723
120.877
1200.027
1210.811
1220.122
1230.181
1240.135
1250.599
1260.474
1270.709
1280.556
1290.437
130.763
1300.99
1310.6
1320.0223
1330.994
1340.339
1350.919
1360.25
1370.397
1380.519
1390.276
140.477
1400.917
1410.522
1420.694
1430.00419
1440.702
1450.262
1460.585
1470.314
1480.139
1490.199
150.0576
1500.889
1510.721
1520.214
1530.817
1540.991
1550.722
1560.276
1570.851
1580.04
1590.412
160.892
1600.51
1610.543
1620.597
1630.219
1640.148
1650.893
1660.446
1670.0592
1680.331
1690.161
170.594
180.0878
190.219
20.119
200.398
210.974
220.23
230.604
240.207
250.473
260.262
270.982
280.458
290.00579
30.0895
300.0785
310.821
320.446
330.276
340.209
350.15
360.0213
370.402
380.874
390.386
40.844
400.51
410.27
420.0688
430.182
440.129
450.278
460.286
470.456
480.374
490.304
50.175
500.571
510.477
520.247
530.964
540.906
550.0357
560.704
570.234
580.377
590.965
60.614
600.978
610.486
620.435
630.95
640.799
650.529
660.155
670.662
680.659
690.482
70.977
700.139
710.0178
720.456
730.499
740.0114
750.0591
760.0771
770.0502
780.338
790.539
80.449
800.303
810.272
820.429
830.187
840.556
850.292
860.336
870.891
880.929
890.519
90.511
900.00213
910.937
920.612
930.407
940.00381
950.671
960.43
970.879
980.901
990.116



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: CNhs11757


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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