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FF:11674-122G9: 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 17:27, 29 March 2012


Name:Smooth Muscle Cells - Tracheal, donor3
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 number2587
catalog numberSC3415
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-0.111
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
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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: CNhs12894

Jaspar motifP-value
MA0002.20.573
MA0003.10.459
MA0004.10.655
MA0006.10.276
MA0007.10.00801
MA0009.10.341
MA0014.10.797
MA0017.10.678
MA0018.22.78849e-4
MA0019.10.219
MA0024.10.00417
MA0025.10.00102
MA0027.10.675
MA0028.12.61895e-6
MA0029.10.562
MA0030.10.996
MA0031.10.761
MA0035.20.227
MA0038.10.101
MA0039.20.311
MA0040.10.157
MA0041.10.309
MA0042.10.332
MA0043.10.00256
MA0046.10.815
MA0047.20.75
MA0048.10.892
MA0050.12.48873e-4
MA0051.10.103
MA0052.10.109
MA0055.10.142
MA0057.10.966
MA0058.10.739
MA0059.10.639
MA0060.11.65978e-5
MA0061.10.132
MA0062.23.27383e-16
MA0065.20.831
MA0066.10.403
MA0067.10.0161
MA0068.10.71
MA0069.10.187
MA0070.10.788
MA0071.10.957
MA0072.10.546
MA0073.10.582
MA0074.10.0583
MA0076.14.61059e-8
MA0077.10.228
MA0078.10.861
MA0079.20.581
MA0080.22.30672e-8
MA0081.10.00746
MA0083.13.25062e-7
MA0084.10.519
MA0087.10.99
MA0088.10.675
MA0090.10.00258
MA0091.13.80951e-5
MA0092.10.765
MA0093.10.892
MA0099.20.0753
MA0100.10.252
MA0101.10.00666
MA0102.20.934
MA0103.10.029
MA0104.20.295
MA0105.10.237
MA0106.10.791
MA0107.10.0012
MA0108.20.00199
MA0111.10.737
MA0112.20.0134
MA0113.10.0137
MA0114.10.657
MA0115.10.235
MA0116.10.386
MA0117.10.186
MA0119.10.016
MA0122.10.75
MA0124.10.539
MA0125.10.624
MA0131.10.109
MA0135.10.627
MA0136.11.63544e-12
MA0137.20.676
MA0138.20.49
MA0139.10.62
MA0140.10.208
MA0141.10.155
MA0142.10.348
MA0143.10.997
MA0144.10.577
MA0145.10.16
MA0146.10.44
MA0147.10.208
MA0148.10.626
MA0149.10.918
MA0150.10.111
MA0152.10.011
MA0153.10.149
MA0154.10.393
MA0155.10.115
MA0156.12.23974e-15
MA0157.10.686
MA0159.10.618
MA0160.10.838
MA0162.10.073
MA0163.10.0435
MA0164.10.765
MA0258.10.245
MA0259.10.291



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: CNhs12894

Novel motifP-value
10.873
100.899
1000.55
1010.538
1020.11
1030.64
1040.611
1050.743
1060.0693
1070.0406
1080.317
1090.57
110.485
1100.23
1110.769
1120.762
1130.0573
1140.483
1150.367
1160.0203
1170.769
1180.899
1190.764
120.427
1200.231
1210.135
1220.14
1230.082
1240.907
1250.252
1260.671
1270.617
1289.43888e-4
1290.996
130.892
1300.916
1310.635
1320.455
1330.799
1340.878
1350.48
1360.615
1370.127
1380.405
1390.402
140.68
1400.768
1410.703
1420.712
1430.718
1440.466
1450.359
1460.501
1470.27
1480.221
1490.0453
150.733
1500.263
1510.187
1520.252
1530.382
1540.364
1550.133
1560.552
1570.715
1580.00226
1590.113
160.035
1600.124
1610.908
1620.0468
1630.504
1640.318
1650.411
1660.0709
1670.208
1680.934
1690.0921
170.507
180.316
190.0103
20.2
200.271
210.0978
220.142
230.0492
240.524
250.312
260.153
270.459
280.0634
290.76
30.624
300.361
310.257
322.49413e-9
330.246
340.436
350.93
360.161
370.278
380.911
390.146
40.203
400.533
410.0289
420.535
430.397
440.819
450.351
460.174
470.583
480.409
490.672
50.923
500.507
510.669
520.146
530.332
540.545
550.616
560.202
570.959
580.367
590.0628
60.719
600.437
610.731
620.814
630.42
640.941
650.225
660.38
670.647
680.76
690.174
70.513
700.81
710.197
720.159
730.344
740.14
750.882
760.788
770.307
780.593
790.0723
80.0647
800.32
810.289
820.339
830.694
840.966
850.0108
860.54
870.669
880.395
890.133
90.334
900.747
910.221
920.0273
930.595
940.782
950.792
960.215
970.253
980.468
995.03515e-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: CNhs12894


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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