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FF:11284-116I6: 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 - Brachiocephalic, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrachiocephalic artery
dev stageNA
sexunknown
ageNA
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 number2463
catalog numbercustom
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-0.219
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-0.324
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: CNhs11086

Jaspar motifP-value
MA0002.20.451
MA0003.10.23
MA0004.10.259
MA0006.10.149
MA0007.10.909
MA0009.10.41
MA0014.10.747
MA0017.10.696
MA0018.20.00156
MA0019.10.171
MA0024.13.2845e-9
MA0025.10.798
MA0027.10.625
MA0028.10.526
MA0029.10.302
MA0030.10.598
MA0031.10.104
MA0035.20.369
MA0038.10.0485
MA0039.20.409
MA0040.10.35
MA0041.10.284
MA0042.10.692
MA0043.10.0478
MA0046.10.738
MA0047.20.299
MA0048.10.309
MA0050.12.10305e-6
MA0051.10.0173
MA0052.10.958
MA0055.10.899
MA0057.10.291
MA0058.10.103
MA0059.10.528
MA0060.18.38906e-6
MA0061.10.615
MA0062.20.0385
MA0065.20.762
MA0066.10.214
MA0067.10.00367
MA0068.10.914
MA0069.10.243
MA0070.10.765
MA0071.10.947
MA0072.10.645
MA0073.10.823
MA0074.10.411
MA0076.10.339
MA0077.10.0181
MA0078.10.0564
MA0079.20.451
MA0080.20.00178
MA0081.10.152
MA0083.14.58892e-6
MA0084.10.303
MA0087.10.324
MA0088.10.488
MA0090.10.00243
MA0091.10.193
MA0092.10.123
MA0093.10.265
MA0099.25.56335e-12
MA0100.10.13
MA0101.10.623
MA0102.20.242
MA0103.10.115
MA0104.20.201
MA0105.10.479
MA0106.10.118
MA0107.10.542
MA0108.23.83048e-4
MA0111.10.0184
MA0112.20.0222
MA0113.10.936
MA0114.10.798
MA0115.10.459
MA0116.10.38
MA0117.10.508
MA0119.10.195
MA0122.10.799
MA0124.10.744
MA0125.10.977
MA0131.10.558
MA0135.10.931
MA0136.10.0742
MA0137.20.122
MA0138.20.597
MA0139.10.785
MA0140.10.706
MA0141.10.452
MA0142.10.963
MA0143.10.786
MA0144.10.633
MA0145.10.168
MA0146.10.48
MA0147.10.537
MA0148.10.319
MA0149.10.972
MA0150.10.261
MA0152.10.281
MA0153.10.768
MA0154.10.256
MA0155.10.0292
MA0156.10.746
MA0157.10.547
MA0159.10.421
MA0160.10.868
MA0162.10.0354
MA0163.10.0113
MA0164.10.555
MA0258.10.182
MA0259.10.615



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: CNhs11086

Novel motifP-value
10.811
100.326
1000.496
1010.731
1020.79
1030.196
1040.406
1050.967
1060.0173
1070.0311
1080.842
1090.127
110.109
1100.325
1110.871
1120.704
1130.109
1140.157
1150.306
1160.052
1170.789
1180.992
1190.537
120.797
1200.16
1210.783
1220.849
1230.014
1240.602
1250.294
1260.743
1270.636
1280.0891
1290.995
130.538
1300.303
1310.185
1320.774
1330.725
1340.177
1350.0133
1360.991
1370.502
1380.21
1390.174
140.582
1400.845
1410.233
1420.704
1430.00659
1440.752
1450.142
1460.845
1470.127
1480.834
1490.0111
150.69
1500.153
1510.468
1520.00939
1530.925
1540.769
1550.0853
1560.868
1570.786
1580.0129
1590.33
160.193
1600.145
1610.756
1620.796
1630.996
1640.46
1650.439
1660.554
1670.624
1680.433
1690.0867
170.257
180.0599
190.0519
20.193
200.36
210.369
220.188
230.0534
240.204
250.376
260.468
270.635
280.164
290.547
30.586
300.339
310.561
325.07616e-5
330.865
340.286
350.514
360.354
370.0978
380.813
390.301
40.703
400.626
410.553
420.711
430.324
440.437
450.188
460.167
470.61
480.379
490.817
50.675
500.335
510.813
520.691
530.48
540.462
550.272
560.551
570.614
580.698
590.0824
60.922
600.645
610.774
620.75
630.162
640.87
650.247
660.964
670.257
680.451
690.794
70.761
700.0502
710.353
720.802
730.00626
740.864
750.527
760.881
770.00603
780.925
790.0584
80.213
800.316
810.547
820.478
830.694
840.862
850.033
860.368
870.0163
880.0604
890.0322
90.206
900.563
910.717
920.36
930.974
940.744
950.253
960.908
970.569
980.689
990.00524



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: CNhs11086


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)
0002589 (smooth muscle cell of the brachiocephalic vasculature)

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)
0001009 (circulatory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001529 (brachiocephalic 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)
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)
0007204 (brachiocephalic vasculature)
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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