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FF:14314-155D3: 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 17:19, 29 March 2012


Name:Smooth Muscle Cells - Aortic, donor0 (nuclear fraction)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueaorta
dev stage54 years old adult
sexmale
age54
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 numberNA
catalog numberCA354-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-penis0.283
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-0.176
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs12402

Jaspar motifP-value
MA0002.20.127
MA0003.10.847
MA0004.10.104
MA0006.10.646
MA0007.10.833
MA0009.10.706
MA0014.10.584
MA0017.10.00668
MA0018.20.203
MA0019.10.994
MA0024.15.23329e-4
MA0025.10.0289
MA0027.10.498
MA0028.10.637
MA0029.10.401
MA0030.10.336
MA0031.10.11
MA0035.20.0236
MA0038.10.0291
MA0039.20.289
MA0040.10.212
MA0041.10.511
MA0042.10.843
MA0043.10.223
MA0046.10.0478
MA0047.20.733
MA0048.10.247
MA0050.11.67165e-4
MA0051.10.00968
MA0052.10.197
MA0055.10.589
MA0057.10.958
MA0058.10.0357
MA0059.10.187
MA0060.15.90864e-7
MA0061.10.00979
MA0062.20.108
MA0065.20.0014
MA0066.10.908
MA0067.10.355
MA0068.10.0316
MA0069.10.0855
MA0070.10.163
MA0071.10.226
MA0072.10.291
MA0073.10.67
MA0074.10.769
MA0076.10.893
MA0077.10.172
MA0078.10.999
MA0079.20.705
MA0080.22.17815e-8
MA0081.10.028
MA0083.10.00188
MA0084.10.332
MA0087.10.935
MA0088.10.375
MA0090.12.32462e-4
MA0091.10.798
MA0092.10.995
MA0093.10.175
MA0099.20.326
MA0100.10.303
MA0101.10.00176
MA0102.20.69
MA0103.12.35231e-4
MA0104.20.0114
MA0105.10.00516
MA0106.10.421
MA0107.10.00341
MA0108.20.0592
MA0111.10.0745
MA0112.20.741
MA0113.10.946
MA0114.10.00148
MA0115.10.026
MA0116.10.486
MA0117.10.907
MA0119.10.906
MA0122.10.731
MA0124.16.0919e-4
MA0125.10.0704
MA0131.10.855
MA0135.10.522
MA0136.14.39297e-8
MA0137.20.226
MA0138.20.584
MA0139.10.635
MA0140.10.091
MA0141.10.033
MA0142.10.00981
MA0143.10.863
MA0144.10.522
MA0145.10.917
MA0146.10.129
MA0147.10.134
MA0148.10.676
MA0149.10.51
MA0150.10.603
MA0152.10.171
MA0153.10.96
MA0154.10.21
MA0155.10.783
MA0156.16.73063e-4
MA0157.10.183
MA0159.10.672
MA0160.10.00318
MA0162.10.175
MA0163.10.0832
MA0164.10.196
MA0258.10.622
MA0259.10.521



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: CNhs12402

Novel motifP-value
10.118
100.169
1000.352
1010.258
1020.327
1030.699
1040.994
1050.228
1060.291
1070.544
1080.397
1090.208
110.437
1100.84
1110.187
1120.875
1130.136
1140.692
1150.395
1160.475
1170.5
1180.956
1190.597
120.641
1200.712
1210.9
1220.0586
1238.98358e-4
1240.0685
1250.398
1260.446
1270.288
1280.104
1290.469
130.166
1300.372
1310.858
1320.847
1330.554
1340.48
1350.301
1360.604
1370.972
1380.607
1390.618
140.216
1400.329
1410.597
1420.761
1430.602
1440.916
1450.392
1460.0238
1470.0592
1480.455
1490.125
150.104
1500.411
1510.719
1520.584
1530.912
1540.678
1550.094
1560.156
1570.859
1580.0923
1590.551
160.308
1600.054
1610.497
1620.822
1630.263
1640.117
1650.293
1660.163
1670.327
1680.497
1690.827
170.795
180.534
190.587
20.874
200.683
210.993
220.963
230.532
240.338
250.095
260.676
270.319
280.339
290.769
30.586
300.608
310.996
325.16482e-11
330.217
340.463
350.682
360.00494
370.986
380.256
390.808
40.133
400.0146
410.0941
420.17
430.295
440.694
450.312
460.543
470.151
480.37
490.05
50.441
500.622
510.266
520.551
530.112
540.288
550.415
560.311
570.574
580.264
590.762
60.751
600.331
610.463
620.125
630.815
640.185
650.561
660.0691
670.571
680.748
690.949
70.055
700.271
710.711
720.133
730.556
740.212
750.587
760.95
770.689
780.0978
790.0605
80.242
800.398
810.371
820.87
830.139
840.166
850.928
860.71
870.877
880.73
890.472
90.9
900.245
910.893
920.677
930.839
940.674
950.533
960.174
970.284
980.0243
990.237



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: CNhs12402


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)
0002539 (aortic smooth muscle cell)

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)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000947 (aorta)
0001009 (circulatory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001135 (smooth muscle tissue)
0001637 (artery)
0001981 (blood vessel)
0002036 (striated muscle tissue)
0002049 (vasculature)
0002050 (embryonic structure)
0002111 (artery smooth muscle tissue)
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)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004178 (aorta smooth muscle tissue)
0004237 (blood vessel smooth muscle)
0004290 (dermomyotome)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004571 (systemic arterial system)
0004572 (arterial system)
0004573 (systemic artery)
0004695 (arterial system smooth muscle)
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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