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FF:11513-119H1: 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 - Tracheal, donor1
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 numberlot:572
catalog numberSC3415
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-0.0357
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-0.344
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: CNhs11329

Jaspar motifP-value
MA0002.20.12
MA0003.10.234
MA0004.10.473
MA0006.10.437
MA0007.10.0304
MA0009.10.404
MA0014.10.999
MA0017.10.0741
MA0018.25.83823e-5
MA0019.10.949
MA0024.14.25106e-4
MA0025.10.0113
MA0027.10.457
MA0028.10.0107
MA0029.10.515
MA0030.10.204
MA0031.10.222
MA0035.20.638
MA0038.10.0471
MA0039.20.844
MA0040.10.286
MA0041.10.283
MA0042.10.781
MA0043.12.6169e-4
MA0046.10.985
MA0047.20.935
MA0048.10.784
MA0050.11.23998e-5
MA0051.10.00458
MA0052.10.657
MA0055.10.595
MA0057.10.075
MA0058.10.465
MA0059.10.309
MA0060.10.00516
MA0061.10.616
MA0062.25.1456e-6
MA0065.20.00803
MA0066.10.0444
MA0067.10.0186
MA0068.10.22
MA0069.10.165
MA0070.10.495
MA0071.10.0259
MA0072.10.374
MA0073.10.948
MA0074.10.173
MA0076.10.00113
MA0077.10.719
MA0078.10.988
MA0079.20.841
MA0080.22.67259e-6
MA0081.10.0685
MA0083.13.31111e-4
MA0084.10.849
MA0087.10.747
MA0088.10.285
MA0090.10.0341
MA0091.10.00217
MA0092.10.149
MA0093.10.527
MA0099.20.00934
MA0100.10.386
MA0101.10.332
MA0102.20.0488
MA0103.10.455
MA0104.20.937
MA0105.10.143
MA0106.10.0221
MA0107.10.441
MA0108.20.177
MA0111.10.711
MA0112.26.76047e-4
MA0113.10.0574
MA0114.10.0655
MA0115.10.338
MA0116.10.113
MA0117.10.434
MA0119.10.0357
MA0122.10.778
MA0124.10.306
MA0125.10.912
MA0131.10.202
MA0135.10.142
MA0136.13.21363e-8
MA0137.20.0886
MA0138.20.0866
MA0139.10.605
MA0140.10.843
MA0141.10.0137
MA0142.10.629
MA0143.10.621
MA0144.10.878
MA0145.10.146
MA0146.10.0635
MA0147.10.751
MA0148.10.56
MA0149.10.366
MA0150.10.548
MA0152.10.333
MA0153.10.0561
MA0154.10.0929
MA0155.10.0915
MA0156.12.6739e-6
MA0157.10.951
MA0159.10.257
MA0160.10.137
MA0162.10.117
MA0163.10.0244
MA0164.10.514
MA0258.10.0169
MA0259.10.888



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: CNhs11329

Novel motifP-value
10.255
100.713
1000.569
1010.782
1020.639
1030.174
1040.452
1050.366
1060.0435
1070.0499
1080.195
1090.115
110.0591
1100.134
1110.344
1120.329
1130.274
1140.131
1150.296
1160.129
1170.616
1180.592
1190.216
120.675
1200.528
1210.811
1220.886
1230.371
1240.148
1250.56
1260.556
1270.194
1280.0314
1290.513
130.497
1300.87
1310.949
1320.553
1330.861
1340.477
1350.123
1360.658
1370.226
1380.583
1390.117
140.885
1400.673
1410.644
1420.723
1430.0284
1440.457
1450.256
1460.537
1470.288
1480.232
1490.00767
150.432
1500.54
1510.344
1520.128
1530.646
1540.381
1550.56
1560.991
1570.433
1580.142
1590.531
160.0556
1600.0248
1610.672
1620.29
1630.814
1640.539
1650.929
1660.723
1670.396
1680.971
1690.0399
170.133
180.0843
190.0448
20.315
200.409
210.122
220.0793
230.127
240.192
250.904
260.0527
270.154
280.287
290.587
30.252
300.305
310.298
321.34589e-6
330.311
340.231
350.6
360.642
370.185
380.319
390.217
40.474
400.0569
410.5
420.54
430.135
440.415
450.403
460.0772
470.255
480.275
490.141
50.713
500.42
510.358
520.258
530.875
540.324
550.246
560.237
570.294
580.865
590.0293
60.982
600.264
610.505
620.631
630.162
640.167
650.0654
660.775
670.806
680.0349
690.0743
70.855
700.0233
710.0693
720.708
730.0804
740.948
750.418
760.758
770.0329
780.843
790.117
80.0172
800.688
810.315
820.169
830.3
840.391
850.057
860.872
870.289
880.266
890.0346
90.258
900.402
910.136
920.0461
930.559
940.164
950.397
960.443
970.517
980.117
990.00371



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: CNhs11329


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)
0002600 (smooth muscle cell of trachea)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
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)
0001004 (respiratory system)
0001005 (respiratory airway)
0001007 (digestive system)
0001015 (musculature)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001555 (digestive tract)
0001558 (lower respiratory 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)
0003126 (trachea)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004290 (dermomyotome)
0004921 (subdivision of digestive tract)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0007026 (primitive gut)
0007196 (tracheobronchial tree)
0008947 (respiratory primordium)
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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