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FF:11366-117I7: 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 17:05, 29 March 2012


Name:Smooth Muscle Cells - Subclavian 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
tissuesubclavian artery
dev stage21 years old adult
sexmale
age21
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 number2139
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-0.102
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-0.192
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs11990

Jaspar motifP-value
MA0002.20.599
MA0003.10.218
MA0004.10.371
MA0006.10.212
MA0007.10.588
MA0009.10.998
MA0014.10.765
MA0017.10.452
MA0018.21.69792e-4
MA0019.10.443
MA0024.11.26211e-4
MA0025.10.231
MA0027.10.538
MA0028.10.0877
MA0029.10.624
MA0030.10.0766
MA0031.10.0267
MA0035.20.369
MA0038.10.0193
MA0039.20.156
MA0040.10.25
MA0041.10.361
MA0042.10.826
MA0043.12.46773e-4
MA0046.10.458
MA0047.20.811
MA0048.10.54
MA0050.10.531
MA0051.10.634
MA0052.10.263
MA0055.10.547
MA0057.10.203
MA0058.10.275
MA0059.10.289
MA0060.12.15691e-7
MA0061.10.263
MA0062.26.18268e-4
MA0065.20.131
MA0066.10.0497
MA0067.10.00198
MA0068.10.265
MA0069.10.182
MA0070.10.579
MA0071.10.97
MA0072.10.995
MA0073.10.677
MA0074.10.0932
MA0076.10.019
MA0077.10.419
MA0078.10.327
MA0079.20.621
MA0080.22.77558e-4
MA0081.10.0725
MA0083.10.175
MA0084.10.202
MA0087.10.861
MA0088.10.945
MA0090.10.00627
MA0091.10.199
MA0092.10.069
MA0093.10.345
MA0099.20.00906
MA0100.10.086
MA0101.10.826
MA0102.20.087
MA0103.10.85
MA0104.20.382
MA0105.10.03
MA0106.10.116
MA0107.10.94
MA0108.20.00153
MA0111.10.566
MA0112.25.00159e-4
MA0113.10.749
MA0114.10.739
MA0115.10.155
MA0116.10.03
MA0117.10.86
MA0119.10.0142
MA0122.10.877
MA0124.10.0361
MA0125.10.683
MA0131.10.382
MA0135.10.417
MA0136.17.62267e-4
MA0137.20.224
MA0138.20.127
MA0139.10.278
MA0140.10.7
MA0141.10.104
MA0142.10.871
MA0143.10.506
MA0144.10.563
MA0145.10.128
MA0146.10.607
MA0147.10.839
MA0148.10.499
MA0149.10.767
MA0150.10.828
MA0152.10.564
MA0153.10.214
MA0154.10.053
MA0155.10.139
MA0156.10.0138
MA0157.10.241
MA0159.10.0305
MA0160.10.906
MA0162.10.0692
MA0163.13.70027e-4
MA0164.10.505
MA0258.10.0199
MA0259.10.743



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: CNhs11990

Novel motifP-value
10.229
100.645
1000.973
1010.848
1020.955
1030.0246
1040.443
1050.296
1060.0219
1070.0259
1080.216
1090.0857
110.0694
1100.203
1110.924
1120.369
1130.169
1140.148
1150.0198
1160.0564
1170.546
1180.46
1190.266
120.456
1200.0446
1210.571
1220.217
1230.193
1240.752
1250.319
1260.623
1270.483
1280.0728
1290.727
130.896
1300.907
1310.651
1320.781
1330.394
1340.529
1350.109
1360.982
1370.424
1380.813
1390.126
140.931
1400.878
1410.857
1420.349
1430.0341
1440.821
1450.122
1460.534
1470.0481
1480.0278
1490.0242
150.288
1500.275
1510.325
1520.0332
1530.613
1540.916
1550.242
1560.739
1570.603
1580.033
1590.307
160.046
1600.0727
1610.682
1620.95
1630.703
1640.0792
1650.971
1660.386
1670.985
1680.542
1690.0258
170.166
180.0764
190.0362
20.32
200.563
210.229
220.227
230.0717
240.699
250.517
260.189
270.415
280.258
290.151
30.247
300.543
310.455
324.64691e-5
330.827
340.772
350.324
360.367
370.0619
380.668
390.292
40.956
400.551
410.507
420.549
430.185
440.0418
450.552
460.0809
470.214
480.273
490.482
50.589
500.69
510.636
520.963
530.425
540.432
550.271
560.536
570.461
580.982
590.0256
60.615
600.306
610.868
620.505
630.158
640.44
650.283
660.789
670.0999
680.701
690.183
70.952
700.0567
710.264
720.923
730.0114
740.289
750.223
760.996
770.00402
780.64
790.00175
80.0517
800.715
810.267
820.309
830.298
840.583
850.0168
860.469
870.0347
880.0978
890.00488
90.485
900.593
910.271
920.0995
930.419
940.339
950.181
960.763
970.725
980.932
990.00966



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: CNhs11990


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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