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FF:11434-118H3: 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 - Carotid, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecarotid 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 number2139
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-0.203
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-0.179
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
C115-pituitary-Neural-caudate-putamen-amygdala-medulla-hippocampus0
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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: CNhs12044

Jaspar motifP-value
MA0002.20.158
MA0003.10.117
MA0004.10.404
MA0006.10.371
MA0007.10.118
MA0009.10.84
MA0014.10.762
MA0017.10.245
MA0018.20.0768
MA0019.10.302
MA0024.10.00395
MA0025.10.799
MA0027.10.622
MA0028.10.341
MA0029.10.59
MA0030.10.36
MA0031.10.0068
MA0035.20.899
MA0038.10.157
MA0039.20.756
MA0040.10.323
MA0041.10.321
MA0042.10.662
MA0043.10.0954
MA0046.10.752
MA0047.20.693
MA0048.10.428
MA0050.10.00241
MA0051.10.181
MA0052.10.926
MA0055.10.396
MA0057.10.393
MA0058.10.226
MA0059.10.235
MA0060.10.0364
MA0061.10.0819
MA0062.20.0446
MA0065.20.00762
MA0066.10.0751
MA0067.10.0433
MA0068.10.388
MA0069.10.43
MA0070.10.846
MA0071.10.158
MA0072.10.605
MA0073.10.433
MA0074.10.0506
MA0076.10.0938
MA0077.10.376
MA0078.10.149
MA0079.20.635
MA0080.20.00153
MA0081.10.0754
MA0083.10.00148
MA0084.10.872
MA0087.10.59
MA0088.10.482
MA0090.10.232
MA0091.10.165
MA0092.10.243
MA0093.10.382
MA0099.25.31862e-10
MA0100.10.0336
MA0101.10.247
MA0102.20.309
MA0103.10.761
MA0104.20.685
MA0105.10.0418
MA0106.10.117
MA0107.10.142
MA0108.24.17613e-5
MA0111.10.121
MA0112.29.93413e-4
MA0113.10.254
MA0114.10.185
MA0115.10.93
MA0116.10.0469
MA0117.10.532
MA0119.10.146
MA0122.10.671
MA0124.10.344
MA0125.10.396
MA0131.10.388
MA0135.10.522
MA0136.10.00382
MA0137.20.0887
MA0138.20.105
MA0139.10.317
MA0140.10.878
MA0141.10.0377
MA0142.10.3
MA0143.10.427
MA0144.10.634
MA0145.10.125
MA0146.10.0827
MA0147.10.776
MA0148.10.59
MA0149.10.256
MA0150.10.0414
MA0152.10.354
MA0153.10.314
MA0154.10.0402
MA0155.10.0701
MA0156.10.271
MA0157.10.115
MA0159.10.139
MA0160.10.285
MA0162.10.0458
MA0163.14.55564e-4
MA0164.10.504
MA0258.17.72176e-4
MA0259.10.501



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: CNhs12044

Novel motifP-value
10.464
100.854
1000.72
1010.127
1020.842
1030.138
1040.323
1050.654
1060.0321
1070.0762
1080.474
1090.0267
110.0466
1100.153
1110.739
1120.514
1130.279
1140.257
1150.0511
1160.0277
1170.31
1180.605
1190.0867
120.971
1200.0643
1210.686
1220.794
1230.0885
1240.636
1250.5
1260.61
1270.571
1280.132
1290.622
130.661
1300.515
1310.659
1320.6
1330.784
1340.781
1350.241
1360.44
1370.696
1380.703
1390.253
140.628
1400.555
1410.94
1420.655
1430.0178
1440.808
1450.116
1460.11
1470.253
1480.862
1490.412
150.561
1500.147
1510.619
1520.0437
1530.192
1540.57
1550.362
1560.831
1570.603
1580.169
1590.738
160.0358
1600.0404
1610.583
1620.696
1630.99
1640.176
1650.122
1660.634
1670.22
1680.86
1690.0404
170.0935
180.0194
190.0708
20.152
200.495
210.366
220.192
230.0573
240.399
250.691
260.0202
270.251
280.234
290.158
30.303
300.558
310.354
321.24549e-7
330.385
340.344
350.395
360.79
370.0885
380.478
390.196
40.533
400.0561
410.882
420.72
430.237
440.124
450.332
460.113
470.346
480.145
490.512
50.855
500.476
510.486
520.744
530.428
540.652
550.496
560.355
570.55
580.925
590.00578
60.706
600.285
610.548
620.554
630.238
640.172
650.0807
660.741
670.351
680.0601
690.17
70.84
700.212
710.138
720.977
730.0163
740.714
750.268
760.688
770.00454
780.454
790.00606
80.104
800.995
810.669
820.827
830.126
840.795
850.0525
860.496
870.0176
880.299
890.0301
90.213
900.803
910.369
920.491
930.989
940.885
950.0181
960.4
970.235
980.675
990.0472



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: CNhs12044


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)
0002596 (smooth muscle cell of the carotid 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)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001009 (circulatory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
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)
0005396 (carotid artery segment)
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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