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FF:11364-117I5: 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 17:04, 29 March 2012


Name:Smooth Muscle Cells - Internal Thoracic Artery, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueinternal thoracic artery
dev stage35 years old adult
sexmale
age35
cell typesmooth muscle cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1678
catalog numberCA358-R10a
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-penis0.0505
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-0.295
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11988

Jaspar motifP-value
MA0002.20.247
MA0003.10.34
MA0004.10.0826
MA0006.10.0567
MA0007.10.342
MA0009.10.51
MA0014.10.415
MA0017.10.784
MA0018.24.72834e-7
MA0019.10.821
MA0024.15.85194e-8
MA0025.10.0545
MA0027.10.766
MA0028.10.94
MA0029.10.857
MA0030.10.0215
MA0031.10.0894
MA0035.20.0348
MA0038.16.83306e-4
MA0039.20.0394
MA0040.10.849
MA0041.10.27
MA0042.10.998
MA0043.13.17679e-4
MA0046.10.0551
MA0047.20.329
MA0048.10.404
MA0050.13.30279e-31
MA0051.15.81013e-28
MA0052.16.1e-4
MA0055.10.28
MA0057.10.974
MA0058.10.0495
MA0059.10.943
MA0060.14.26725e-17
MA0061.10.0463
MA0062.20.0221
MA0065.20.33
MA0066.10.33
MA0067.10.00116
MA0068.10.439
MA0069.10.309
MA0070.10.819
MA0071.10.24
MA0072.10.158
MA0073.10.629
MA0074.10.0842
MA0076.10.51
MA0077.10.623
MA0078.10.511
MA0079.20.644
MA0080.22.10453e-4
MA0081.10.102
MA0083.10.552
MA0084.10.22
MA0087.10.843
MA0088.10.632
MA0090.10.0452
MA0091.10.4
MA0092.10.228
MA0093.10.0744
MA0099.20.883
MA0100.10.0163
MA0101.10.26
MA0102.20.812
MA0103.10.033
MA0104.20.0675
MA0105.10.0333
MA0106.10.168
MA0107.10.0724
MA0108.20.247
MA0111.10.199
MA0112.20.0419
MA0113.10.724
MA0114.10.873
MA0115.10.837
MA0116.10.161
MA0117.10.1
MA0119.10.0563
MA0122.10.863
MA0124.10.13
MA0125.10.11
MA0131.10.224
MA0135.10.112
MA0136.13.97994e-4
MA0137.20.0389
MA0138.20.566
MA0139.10.789
MA0140.10.022
MA0141.10.866
MA0142.10.0807
MA0143.10.749
MA0144.10.0405
MA0145.10.397
MA0146.10.867
MA0147.10.263
MA0148.10.818
MA0149.10.794
MA0150.10.388
MA0152.10.316
MA0153.10.0995
MA0154.10.242
MA0155.10.215
MA0156.10.0777
MA0157.10.492
MA0159.10.141
MA0160.10.28
MA0162.10.0395
MA0163.12.21509e-4
MA0164.10.445
MA0258.10.34
MA0259.10.136



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: CNhs11988

Novel motifP-value
10.867
100.427
1000.926
1010.504
1020.881
1030.244
1040.668
1050.0522
1060.0388
1070.103
1080.617
1090.467
110.473
1100.323
1110.856
1120.3
1130.0511
1140.594
1150.137
1160.0595
1170.261
1180.621
1190.901
120.363
1200.119
1210.999
1220.143
1230.362
1240.332
1250.183
1260.885
1270.941
1280.112
1290.75
130.825
1300.628
1310.529
1320.435
1330.684
1340.846
1350.568
1360.728
1370.988
1380.759
1390.349
140.319
1400.933
1410.441
1420.806
1430.631
1440.621
1450.902
1460.576
1470.00642
1480.408
1490.247
150.684
1500.0604
1510.446
1520.0234
1530.222
1540.905
1550.0403
1560.793
1570.444
1580.0119
1590.262
160.0311
1600.644
1610.985
1620.703
1630.692
1640.00681
1650.515
1660.106
1670.36
1680.817
1690.118
170.291
180.128
190.145
20.168
200.763
210.301
220.409
230.157
240.546
250.0947
260.767
270.65
280.277
290.097
30.17
300.702
310.738
329.69612e-7
330.533
340.965
350.774
360.276
370.0207
380.998
390.104
40.0348
400.163
410.718
420.92
430.318
440.213
450.779
460.664
470.989
480.86
490.255
50.957
500.472
510.805
520.993
530.271
540.751
550.0982
560.543
570.776
580.469
590.176
60.983
600.344
610.632
620.754
630.339
640.728
650.24
660.139
670.166
680.885
690.64
70.174
700.543
710.596
720.656
730.0118
740.287
750.221
760.315
770.00998
780.744
790.032
80.409
800.405
810.806
820.55
830.975
840.617
850.0958
860.346
870.00675
880.475
890.0112
90.382
900.713
910.76
920.259
930.836
940.803
950.155
960.476
970.428
980.859
990.00835



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: CNhs11988


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000056 (myoblast)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000359 (vascular associated smooth muscle cell)
0000393 (electrically responsive cell)
0000514 (smooth muscle myoblast)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002593 (smooth muscle cell of the internal thoracic artery)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001009 (circulatory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001533 (subclavian artery)
0001637 (artery)
0001981 (blood vessel)
0002036 (striated muscle tissue)
0002049 (vasculature)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002456 (internal thoracic artery)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003081 (lateral plate mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0003509 (arterial blood vessel)
0003834 (thoracic segment blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004571 (systemic arterial system)
0004572 (arterial system)
0004573 (systemic artery)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006965 (vascular cord)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
0009142 (entire embryonic mesenchyme)

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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