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FF:11438-118H7: 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 17:08, 29 March 2012


Name:Smooth Muscle Cells - Subclavian Artery, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesubclavian artery
dev stage59 years old adult
sexmale
age59
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 number2115
catalog numberCA3010-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-penis-0.178
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-0.379
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
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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: CNhs12048

Jaspar motifP-value
MA0002.20.784
MA0003.10.198
MA0004.10.111
MA0006.10.129
MA0007.10.614
MA0009.10.868
MA0014.10.753
MA0017.10.892
MA0018.24.98701e-4
MA0019.10.262
MA0024.16.98271e-10
MA0025.10.454
MA0027.10.488
MA0028.10.184
MA0029.10.771
MA0030.10.267
MA0031.10.0186
MA0035.20.217
MA0038.10.00104
MA0039.20.285
MA0040.10.255
MA0041.10.171
MA0042.10.565
MA0043.15.01694e-4
MA0046.10.616
MA0047.20.98
MA0048.10.613
MA0050.10.00548
MA0051.16.91852e-5
MA0052.10.522
MA0055.10.528
MA0057.10.252
MA0058.10.0454
MA0059.10.741
MA0060.13.05271e-9
MA0061.10.374
MA0062.20.00426
MA0065.20.466
MA0066.10.353
MA0067.10.0173
MA0068.10.819
MA0069.10.38
MA0070.10.351
MA0071.10.862
MA0072.10.827
MA0073.10.849
MA0074.10.292
MA0076.10.0622
MA0077.10.28
MA0078.10.292
MA0079.20.332
MA0080.20.00165
MA0081.10.0972
MA0083.10.0238
MA0084.10.14
MA0087.10.393
MA0088.10.892
MA0090.10.00223
MA0091.10.424
MA0092.10.136
MA0093.10.0959
MA0099.20.0115
MA0100.10.0466
MA0101.10.933
MA0102.20.193
MA0103.10.449
MA0104.20.0683
MA0105.10.257
MA0106.10.152
MA0107.10.716
MA0108.23.29022e-4
MA0111.10.02
MA0112.20.00842
MA0113.10.998
MA0114.10.77
MA0115.10.297
MA0116.10.315
MA0117.10.373
MA0119.10.0709
MA0122.10.748
MA0124.10.141
MA0125.10.271
MA0131.10.607
MA0135.10.55
MA0136.10.0107
MA0137.20.448
MA0138.20.511
MA0139.10.347
MA0140.10.365
MA0141.10.422
MA0142.10.349
MA0143.10.978
MA0144.10.308
MA0145.10.162
MA0146.10.425
MA0147.10.311
MA0148.10.537
MA0149.10.905
MA0150.10.876
MA0152.10.616
MA0153.10.672
MA0154.10.16
MA0155.10.0527
MA0156.10.172
MA0157.10.389
MA0159.10.113
MA0160.10.732
MA0162.10.0286
MA0163.10.0115
MA0164.10.447
MA0258.10.121
MA0259.10.896



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: CNhs12048

Novel motifP-value
10.876
100.833
1000.467
1010.277
1020.775
1030.0333
1040.432
1050.465
1060.0484
1070.0689
1080.693
1090.121
110.142
1100.638
1110.76
1120.351
1130.0625
1140.108
1150.0487
1160.0332
1170.5
1180.546
1190.596
120.623
1200.0824
1210.97
1220.336
1230.00867
1240.522
1250.557
1260.625
1270.69
1280.134
1290.97
130.653
1300.85
1310.339
1320.726
1330.381
1340.775
1350.0544
1360.407
1370.828
1380.587
1390.0815
140.481
1400.839
1410.668
1420.574
1430.0895
1440.592
1450.626
1460.795
1470.0723
1480.56
1490.0377
150.86
1500.164
1510.569
1520.0253
1530.242
1540.951
1550.166
1560.639
1570.607
1580.0277
1590.309
160.0381
1600.19
1610.663
1620.954
1630.757
1640.176
1650.741
1660.0496
1670.468
1680.31
1690.0834
170.163
180.0627
190.0487
20.2
200.427
210.41
220.184
230.0481
240.362
250.312
260.886
270.447
280.206
290.169
30.426
300.274
310.525
325.34805e-5
330.959
340.686
350.541
360.0674
370.0788
380.731
390.171
40.701
400.736
410.336
420.959
430.328
440.161
450.41
460.31
470.442
480.384
490.777
50.664
500.748
510.733
520.897
530.24
540.5
550.265
560.642
570.788
580.836
590.0156
60.873
600.492
610.928
620.648
630.275
640.974
650.19
660.284
670.212
680.695
690.52
70.592
700.0371
710.547
720.923
730.0055
740.728
750.326
760.817
770.00217
780.895
790.012
80.156
800.717
810.771
820.573
830.905
840.608
850.0254
860.365
870.00644
880.368
890.0105
90.264
900.823
910.6
920.357
930.464
940.907
950.249
960.699
970.805
980.754
990.0341



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: CNhs12048


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)
0002595 (smooth muscle cell of the subclavian 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)
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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