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FF:11436-118H5: 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 - Internal Thoracic 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
tissueinternal thoracic artery
dev stage50 years old adult
sexmale
age50
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 number1555
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-penis-0.17
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-0.253
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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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: CNhs12046

Jaspar motifP-value
MA0002.20.128
MA0003.10.153
MA0004.10.321
MA0006.10.261
MA0007.10.204
MA0009.10.439
MA0014.10.69
MA0017.10.186
MA0018.20.00331
MA0019.10.761
MA0024.14.21099e-4
MA0025.10.518
MA0027.10.749
MA0028.10.325
MA0029.10.497
MA0030.10.116
MA0031.10.0248
MA0035.20.549
MA0038.10.0106
MA0039.20.557
MA0040.10.676
MA0041.10.286
MA0042.10.738
MA0043.10.00579
MA0046.10.384
MA0047.20.821
MA0048.10.591
MA0050.12.8996e-5
MA0051.10.022
MA0052.10.619
MA0055.10.874
MA0057.10.159
MA0058.10.18
MA0059.10.272
MA0060.19.8854e-5
MA0061.10.321
MA0062.20.032
MA0065.20.0157
MA0066.10.0701
MA0067.10.0191
MA0068.10.19
MA0069.10.35
MA0070.10.964
MA0071.10.346
MA0072.10.395
MA0073.10.519
MA0074.10.0852
MA0076.10.151
MA0077.10.882
MA0078.10.318
MA0079.20.992
MA0080.20.00203
MA0081.10.19
MA0083.10.00314
MA0084.10.549
MA0087.10.871
MA0088.10.41
MA0090.10.0994
MA0091.10.0362
MA0092.10.0843
MA0093.10.281
MA0099.22.52545e-6
MA0100.10.171
MA0101.10.975
MA0102.20.301
MA0103.10.622
MA0104.20.528
MA0105.10.056
MA0106.10.0921
MA0107.10.883
MA0108.20.0332
MA0111.10.379
MA0112.29.55821e-4
MA0113.10.232
MA0114.10.194
MA0115.10.789
MA0116.10.0288
MA0117.10.789
MA0119.10.0568
MA0122.10.962
MA0124.10.537
MA0125.10.271
MA0131.10.242
MA0135.10.0975
MA0136.10.00136
MA0137.20.0705
MA0138.20.0862
MA0139.10.379
MA0140.10.888
MA0141.10.119
MA0142.10.45
MA0143.10.877
MA0144.10.524
MA0145.10.161
MA0146.10.104
MA0147.10.849
MA0148.10.739
MA0149.10.0963
MA0150.10.267
MA0152.10.877
MA0153.10.705
MA0154.10.0451
MA0155.10.0545
MA0156.10.19
MA0157.10.346
MA0159.10.0402
MA0160.10.623
MA0162.10.0874
MA0163.12.54181e-4
MA0164.10.271
MA0258.10.0142
MA0259.10.81



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: CNhs12046

Novel motifP-value
10.188
100.626
1000.828
1010.186
1020.943
1030.0564
1040.442
1050.988
1060.0196
1070.0493
1080.425
1090.0297
110.0369
1100.139
1110.443
1120.238
1130.322
1140.0426
1150.0367
1160.0877
1170.344
1180.395
1190.184
120.586
1200.0679
1210.737
1220.981
1230.29
1240.294
1250.882
1260.81
1270.243
1280.0536
1290.478
130.813
1300.994
1310.808
1320.904
1330.715
1340.708
1350.01
1360.724
1370.721
1380.91
1390.0673
140.874
1400.93
1410.845
1420.196
1430.00503
1440.954
1450.453
1460.25
1470.178
1480.328
1490.0344
150.361
1500.33
1510.314
1520.0437
1530.715
1540.841
1550.524
1560.167
1570.871
1580.259
1590.595
160.0762
1600.133
1610.241
1620.835
1630.875
1640.311
1650.822
1660.546
1670.765
1680.318
1690.0354
170.215
180.0192
190.0548
20.21
200.471
210.515
220.124
230.0517
240.249
250.965
260.0964
270.236
280.483
290.241
30.24
300.553
310.41
323.73533e-4
330.641
340.355
350.314
360.626
370.0826
380.448
390.364
40.56
400.169
410.244
420.597
430.218
440.0863
450.337
460.0716
470.223
480.143
490.302
50.392
500.369
510.639
520.526
530.797
540.537
550.224
560.372
570.407
580.836
590.0144
60.663
600.208
610.717
620.353
630.139
640.309
650.0777
660.791
670.564
680.115
690.246
70.711
700.0572
710.125
720.7
730.0215
740.814
750.19
760.892
770.0107
780.916
791.54768e-4
80.0394
800.768
810.374
820.338
830.594
840.597
850.0393
860.427
870.0868
880.209
890.0145
90.194
900.632
910.242
920.128
930.176
940.309
950.0319
960.48
970.654
980.791
990.0306



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: CNhs12046


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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