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FF:11289-117A2: 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 16:39, 29 March 2012


Name:Smooth Muscle Cells - Subclavian Artery, donor1
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 stage27 years old adult
sexfemale
age27
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 number2105
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-0.17
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-lymphoma0.0414
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11090

Jaspar motifP-value
MA0002.20.605
MA0003.10.45
MA0004.10.435
MA0006.10.671
MA0007.10.187
MA0009.10.339
MA0014.10.433
MA0017.10.129
MA0018.20.12
MA0019.10.177
MA0024.10.468
MA0025.10.535
MA0027.10.611
MA0028.10.191
MA0029.10.641
MA0030.10.439
MA0031.10.538
MA0035.20.779
MA0038.10.367
MA0039.20.608
MA0040.10.579
MA0041.10.44
MA0042.10.626
MA0043.10.0706
MA0046.10.198
MA0047.20.387
MA0048.10.248
MA0050.11.29006e-5
MA0051.10.0028
MA0052.10.776
MA0055.10.305
MA0057.10.575
MA0058.10.388
MA0059.10.742
MA0060.10.209
MA0061.10.139
MA0062.20.0192
MA0065.20.0483
MA0066.10.966
MA0067.10.201
MA0068.10.731
MA0069.10.952
MA0070.10.163
MA0071.10.706
MA0072.10.515
MA0073.10.707
MA0074.10.332
MA0076.10.419
MA0077.10.219
MA0078.10.439
MA0079.20.169
MA0080.22.54584e-5
MA0081.10.22
MA0083.11.67388e-4
MA0084.10.218
MA0087.10.38
MA0088.10.969
MA0090.10.0284
MA0091.10.597
MA0092.10.555
MA0093.10.592
MA0099.25.5049e-10
MA0100.10.209
MA0101.10.0926
MA0102.20.794
MA0103.10.00105
MA0104.20.0807
MA0105.10.11
MA0106.10.805
MA0107.10.167
MA0108.24.36734e-8
MA0111.10.0379
MA0112.20.739
MA0113.10.444
MA0114.10.0405
MA0115.10.107
MA0116.10.282
MA0117.10.581
MA0119.10.672
MA0122.10.917
MA0124.10.835
MA0125.10.331
MA0131.10.607
MA0135.10.609
MA0136.10.00276
MA0137.20.541
MA0138.20.263
MA0139.10.516
MA0140.10.605
MA0141.10.623
MA0142.10.574
MA0143.10.235
MA0144.10.492
MA0145.10.474
MA0146.10.14
MA0147.10.375
MA0148.10.57
MA0149.10.583
MA0150.10.224
MA0152.10.678
MA0153.10.207
MA0154.10.47
MA0155.10.0558
MA0156.10.03
MA0157.10.26
MA0159.10.547
MA0160.10.67
MA0162.10.239
MA0163.10.367
MA0164.10.351
MA0258.10.947
MA0259.10.562



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: CNhs11090

Novel motifP-value
10.158
100.0834
1000.335
1010.0533
1020.767
1030.86
1040.263
1050.973
1060.961
1070.652
1080.866
1090.8
110.874
1100.924
1110.028
1120.399
1130.0569
1140.976
1150.485
1160.115
1170.334
1180.368
1190.433
120.727
1200.968
1210.357
1220.925
1230.00132
1240.682
1250.608
1260.433
1270.621
1280.674
1290.832
130.0786
1300.0236
1310.36
1320.913
1330.344
1340.696
1350.844
1360.817
1370.483
1380.321
1390.827
140.312
1400.0863
1410.00673
1420.974
1430.126
1440.964
1450.367
1460.113
1470.23
1480.116
1490.635
150.279
1500.442
1510.835
1520.0204
1530.489
1540.481
1550.59
1560.75
1570.88
1580.023
1590.346
160.533
1600.821
1610.954
1620.352
1630.839
1640.638
1650.312
1660.813
1670.305
1680.399
1690.2
170.63
180.515
190.605
20.436
200.249
210.532
220.369
230.424
240.542
250.179
260.246
270.788
280.0595
290.257
30.544
300.217
310.919
326.66898e-6
330.817
340.358
350.454
360.0563
370.977
380.708
390.225
40.903
400.983
410.418
420.926
430.649
440.337
450.618
460.618
470.519
480.85
490.0622
50.657
500.592
510.7
520.525
530.0577
540.614
550.686
560.699
570.641
580.193
590.596
60.883
600.17
610.289
620.237
630.963
640.717
650.717
660.39
670.808
680.00748
690.321
70.269
700.422
710.85
720.658
730.0207
740.843
750.709
760.236
770.379
780.202
790.309
80.803
800.734
810.546
820.301
830.586
840.463
850.984
860.63
870.0831
880.111
890.544
90.378
900.213
910.888
920.175
930.661
940.523
950.492
960.596
970.365
980.612
990.0122



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: CNhs11090


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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