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FF:11508-119G5: 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 16:45, 29 March 2012


Name:Smooth Muscle Cells - Esophageal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueesophagus
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 numberlot:575
catalog numberSC2715
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-0.0557
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-lymphoma0.00953
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
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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: CNhs11324

Jaspar motifP-value
MA0002.20.692
MA0003.10.307
MA0004.10.298
MA0006.10.472
MA0007.10.0137
MA0009.10.257
MA0014.10.946
MA0017.10.244
MA0018.20.0566
MA0019.10.94
MA0024.10.611
MA0025.10.567
MA0027.10.623
MA0028.10.112
MA0029.10.421
MA0030.10.151
MA0031.10.0388
MA0035.20.235
MA0038.10.00442
MA0039.20.389
MA0040.10.271
MA0041.10.426
MA0042.10.87
MA0043.10.0745
MA0046.10.0214
MA0047.20.72
MA0048.10.376
MA0050.10.00213
MA0051.10.00817
MA0052.10.0552
MA0055.10.00979
MA0057.10.352
MA0058.10.378
MA0059.10.23
MA0060.12.06037e-5
MA0061.10.616
MA0062.28.94233e-4
MA0065.20.0709
MA0066.10.401
MA0067.10.0155
MA0068.10.619
MA0069.10.618
MA0070.10.0121
MA0071.10.0767
MA0072.10.737
MA0073.10.871
MA0074.10.449
MA0076.10.0226
MA0077.10.515
MA0078.10.81
MA0079.20.993
MA0080.26.19773e-6
MA0081.10.0296
MA0083.11.28316e-6
MA0084.10.632
MA0087.10.442
MA0088.10.194
MA0090.10.0021
MA0091.18.84785e-4
MA0092.10.216
MA0093.10.34
MA0099.20.161
MA0100.10.333
MA0101.10.761
MA0102.20.308
MA0103.10.958
MA0104.20.872
MA0105.10.565
MA0106.10.166
MA0107.10.647
MA0108.28.00952e-11
MA0111.10.382
MA0112.20.0168
MA0113.10.00632
MA0114.10.0755
MA0115.10.524
MA0116.10.226
MA0117.10.452
MA0119.10.144
MA0122.10.605
MA0124.10.799
MA0125.10.0963
MA0131.10.477
MA0135.10.225
MA0136.17.72742e-7
MA0137.20.0651
MA0138.20.465
MA0139.10.804
MA0140.10.24
MA0141.10.0117
MA0142.10.515
MA0143.10.245
MA0144.10.391
MA0145.10.226
MA0146.10.0288
MA0147.10.695
MA0148.10.484
MA0149.10.599
MA0150.10.666
MA0152.10.818
MA0153.10.0579
MA0154.10.172
MA0155.10.0798
MA0156.14.25189e-5
MA0157.10.17
MA0159.10.946
MA0160.10.163
MA0162.10.154
MA0163.10.174
MA0164.10.751
MA0258.10.0395
MA0259.10.861



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: CNhs11324

Novel motifP-value
10.925
100.615
1000.13
1010.288
1020.62
1030.897
1040.127
1050.029
1060.118
1070.0328
1080.681
1090.0569
110.0414
1100.0978
1110.725
1120.626
1130.93
1140.948
1150.929
1160.0473
1170.828
1180.603
1190.854
120.371
1200.523
1210.266
1220.789
1230.0465
1240.406
1250.284
1260.531
1270.866
1280.346
1290.808
130.289
1300.177
1310.683
1320.548
1330.264
1340.161
1350.285
1360.842
1370.073
1380.0357
1390.715
140.906
1400.567
1410.563
1420.11
1430.376
1440.441
1450.284
1460.254
1470.379
1480.379
1490.317
150.673
1500.496
1510.539
1520.108
1530.069
1540.212
1550.395
1560.473
1570.282
1580.18
1590.886
160.168
1600.0544
1610.244
1620.0647
1630.954
1640.637
1650.0801
1660.931
1670.149
1680.618
1690.0884
170.158
180.242
190.0968
20.451
200.56
210.883
220.105
230.585
240.54
250.565
260.00642
270.476
280.146
290.986
30.78
300.127
310.357
321.95543e-6
330.436
340.0913
350.575
360.661
370.593
380.438
390.484
40.438
400.00547
410.265
420.568
430.274
440.65
450.344
460.177
470.23
480.108
490.177
50.734
500.32
510.328
520.521
530.673
540.636
550.606
560.184
570.514
580.342
590.052
60.375
600.54
610.652
620.497
630.317
640.107
650.0615
660.203
670.948
680.0603
690.15
70.728
700.861
710.0728
720.584
730.0642
740.745
750.696
760.633
770.0306
780.576
790.378
80.0288
800.827
810.852
820.692
830.857
840.377
850.373
860.905
870.27
880.18
890.291
90.176
900.0254
910.359
920.426
930.538
940.203
950.343
960.953
970.545
980.629
996.57564e-4



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: CNhs11324


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)
0002599 (smooth muscle cell of the esophagus)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
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)
0001007 (digestive system)
0001015 (musculature)
0001041 (foregut)
0001043 (esophagus)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001555 (digestive tract)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
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)
0004185 (endodermal part of digestive tract)
0004290 (dermomyotome)
0004921 (subdivision of digestive tract)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)
0009143 (esophageal region)

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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