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FF:11592-120G8: 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 17:17, 29 March 2012


Name:Smooth Muscle Cells - Bronchial, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexNA
ageNA
cell typesmooth muscle cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC3405
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-0.117
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-0.416
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: CNhs12348

Jaspar motifP-value
MA0002.20.0919
MA0003.10.425
MA0004.10.331
MA0006.10.676
MA0007.10.185
MA0009.10.0757
MA0014.10.485
MA0017.10.469
MA0018.23.14925e-6
MA0019.10.565
MA0024.13.0315e-6
MA0025.13.19086e-4
MA0027.10.811
MA0028.12.5951e-5
MA0029.10.613
MA0030.10.56
MA0031.10.875
MA0035.20.225
MA0038.10.0191
MA0039.20.00366
MA0040.10.691
MA0041.10.376
MA0042.10.574
MA0043.16.14439e-4
MA0046.10.814
MA0047.20.848
MA0048.10.288
MA0050.10.0837
MA0051.10.284
MA0052.10.147
MA0055.10.193
MA0057.10.802
MA0058.10.189
MA0059.10.8
MA0060.12.11951e-9
MA0061.10.209
MA0062.24.84364e-14
MA0065.20.584
MA0066.10.804
MA0067.10.0337
MA0068.10.431
MA0069.10.294
MA0070.10.159
MA0071.10.276
MA0072.10.869
MA0073.10.317
MA0074.10.308
MA0076.11.24933e-6
MA0077.10.154
MA0078.10.81
MA0079.20.38
MA0080.22.9034e-9
MA0081.10.00107
MA0083.10.0609
MA0084.10.96
MA0087.10.845
MA0088.10.146
MA0090.10.0284
MA0091.10.00303
MA0092.10.384
MA0093.10.317
MA0099.20.00887
MA0100.10.735
MA0101.10.0151
MA0102.20.468
MA0103.10.00458
MA0104.20.996
MA0105.10.63
MA0106.10.68
MA0107.10.0212
MA0108.20.511
MA0111.10.806
MA0112.20.316
MA0113.10.0208
MA0114.10.61
MA0115.10.625
MA0116.10.722
MA0117.10.142
MA0119.10.0525
MA0122.10.996
MA0124.10.263
MA0125.10.533
MA0131.10.219
MA0135.10.467
MA0136.13.55384e-13
MA0137.20.436
MA0138.20.623
MA0139.10.996
MA0140.10.535
MA0141.10.768
MA0142.10.818
MA0143.10.0586
MA0144.10.0944
MA0145.10.093
MA0146.10.52
MA0147.10.696
MA0148.10.951
MA0149.10.261
MA0150.10.0399
MA0152.10.00605
MA0153.10.112
MA0154.10.829
MA0155.10.561
MA0156.12.75907e-12
MA0157.10.918
MA0159.10.675
MA0160.10.793
MA0162.10.16
MA0163.10.277
MA0164.10.983
MA0258.10.67
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: CNhs12348

Novel motifP-value
10.646
100.566
1000.641
1010.803
1020.0402
1030.108
1040.475
1050.936
1060.174
1070.00636
1080.101
1090.572
110.828
1100.268
1110.724
1120.941
1130.417
1140.693
1150.148
1160.0618
1170.479
1180.402
1190.423
120.457
1200.11
1210.268
1220.145
1231.08628e-4
1240.856
1250.218
1260.548
1270.847
1280.0687
1290.368
130.178
1300.707
1310.413
1320.804
1330.148
1340.682
1350.945
1360.944
1370.0318
1380.932
1390.59
140.229
1400.159
1410.305
1420.856
1430.988
1440.335
1450.805
1460.691
1470.231
1480.541
1490.0754
150.865
1500.578
1510.876
1520.644
1530.219
1540.279
1550.033
1560.221
1570.0954
1580.191
1590.422
160.0883
1600.498
1610.619
1620.0962
1630.893
1640.204
1650.872
1660.0518
1670.274
1680.809
1690.149
170.705
180.0772
190.00482
20.286
200.423
210.206
220.136
230.0233
240.396
250.0989
260.442
270.666
280.119
290.804
30.962
300.415
310.188
322.46237e-7
330.597
340.409
350.789
360.0383
370.756
380.426
390.462
40.116
400.0235
410.193
420.416
430.406
440.295
450.682
460.429
470.424
480.471
490.795
50.873
500.935
510.614
520.419
530.0214
540.25
550.252
560.349
570.626
580.222
590.19
60.572
600.785
610.459
620.739
630.861
640.458
650.321
660.52
670.788
680.575
690.407
70.196
700.0623
710.758
720.428
730.802
740.284
750.267
760.71
770.772
780.257
790.135
80.5
800.321
810.291
820.667
830.274
840.184
850.0213
860.767
870.15
880.289
890.355
90.222
900.789
910.478
920.0199
930.579
940.176
950.47
960.741
970.313
980.584
990.00281



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: CNhs12348


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)
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)
0002598 (bronchial smooth muscle cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000119 (cell layer)
0000383 (musculature of body)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
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)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001558 (lower respiratory tract)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002185 (bronchus)
0002204 (musculoskeletal system)
0002224 (thoracic cavity)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007196 (tracheobronchial tree)
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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