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FF:10079-102A7: 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 16:53, 29 March 2012


Name:left atrium, adult, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueleft atrium
dev stage40 years old adult
sexmale
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 number8060182
catalog numberCat:AM6854
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-penis0.541
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-0.288
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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: CNhs11790

Jaspar motifP-value
MA0002.20.0172
MA0003.10.106
MA0004.10.0324
MA0006.10.388
MA0007.10.815
MA0009.10.244
MA0014.10.467
MA0017.10.376
MA0018.20.00384
MA0019.10.0719
MA0024.10.0183
MA0025.10.229
MA0027.10.756
MA0028.14.08711e-8
MA0029.10.333
MA0030.10.169
MA0031.10.421
MA0035.20.0487
MA0038.10.0123
MA0039.20.0475
MA0040.10.631
MA0041.10.209
MA0042.10.531
MA0043.18.13557e-6
MA0046.10.00411
MA0047.20.0551
MA0048.10.00368
MA0050.10.227
MA0051.10.29
MA0052.14.00945e-27
MA0055.15.57916e-4
MA0057.10.354
MA0058.10.0245
MA0059.10.0141
MA0060.12.85966e-6
MA0061.15.95613e-4
MA0062.25.14143e-15
MA0065.20.28
MA0066.10.419
MA0067.10.149
MA0068.10.591
MA0069.10.792
MA0070.10.766
MA0071.10.109
MA0072.10.688
MA0073.10.815
MA0074.10.674
MA0076.11.33596e-10
MA0077.10.893
MA0078.10.836
MA0079.20.312
MA0080.22.67487e-4
MA0081.10.031
MA0083.17.91336e-4
MA0084.10.981
MA0087.10.659
MA0088.10.0118
MA0090.10.0203
MA0091.10.0632
MA0092.10.119
MA0093.10.0273
MA0099.25.15354e-25
MA0100.10.0132
MA0101.10.00895
MA0102.20.125
MA0103.10.32
MA0104.21.95237e-4
MA0105.18.61399e-5
MA0106.10.0592
MA0107.10.00366
MA0108.22.09717e-10
MA0111.10.524
MA0112.20.0615
MA0113.10.0693
MA0114.10.993
MA0115.10.268
MA0116.10.0732
MA0117.10.118
MA0119.10.468
MA0122.10.428
MA0124.10.589
MA0125.10.741
MA0131.10.0232
MA0135.10.773
MA0136.19.43921e-11
MA0137.20.214
MA0138.20.0166
MA0139.10.117
MA0140.10.807
MA0141.12.74322e-4
MA0142.10.00534
MA0143.10.304
MA0144.10.703
MA0145.10.283
MA0146.10.426
MA0147.12.08073e-4
MA0148.10.926
MA0149.10.517
MA0150.13.10151e-4
MA0152.10.449
MA0153.10.94
MA0154.10.924
MA0155.10.033
MA0156.11.7627e-11
MA0157.10.42
MA0159.10.178
MA0160.10.0143
MA0162.10.35
MA0163.10.0302
MA0164.10.558
MA0258.10.0343
MA0259.10.0344



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: CNhs11790

Novel motifP-value
10.798
100.105
1000.441
1010.83
1020.684
1030.977
1040.267
1050.777
1060.275
1070.0285
1080.152
1090.381
110.932
1100.378
1110.386
1120.153
1130.136
1140.776
1150.0414
1160.156
1170.0103
1180.0219
1190.0801
120.323
1200.187
1210.701
1220.222
1230.0165
1240.908
1250.857
1260.459
1270.732
1280.0818
1290.326
130.101
1300.728
1310.181
1320.0424
1330.0223
1340.0469
1350.0602
1360.147
1370.669
1380.23
1390.38
140.807
1400.329
1410.52
1420.862
1430.333
1440.417
1450.614
1460.718
1470.00465
1480.158
1490.036
150.251
1500.896
1510.414
1520.237
1530.476
1540.838
1550.881
1560.889
1570.98
1580.276
1590.594
160.941
1600.395
1610.422
1620.903
1630.501
1640.0769
1650.281
1660.013
1670.23
1680.295
1690.217
170.951
180.812
190.0323
20.0406
200.00672
210.823
220.29
230.0548
240.0405
250.295
260.175
270.194
280.254
290.0341
30.583
300.105
310.57
320.455
330.135
340.117
350.888
360.184
370.676
380.87
390.0996
40.33
400.0376
410.93
420.17
430.673
440.0437
450.15
460.825
470.515
480.394
490.712
50.952
500.977
510.946
520.161
530.767
540.479
550.582
560.541
570.153
580.736
590.207
60.75
600.389
610.17
620.977
630.906
640.772
650.283
660.0027
670.744
680.248
690.811
70.393
700.352
710.218
720.762
730.729
740.569
750.0329
760.0569
770.0196
780.815
790.0362
80.748
800.764
810.686
820.092
830.517
840.264
850.0455
860.539
870.0406
880.969
890.0538
90.424
900.207
910.0547
920.312
930.474
940.131
950.0453
960.606
970.809
980.975
990.108



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: CNhs11790


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
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002079 (left cardiac atrium)
0002081 (cardiac atrium)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004151 (cardiac chamber)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0007005 (cardiac mesoderm)
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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