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FF:10841-111E4: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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chr19:58144529..58144579,+!0.29!8.80;;chr19:58459047..58459083,-!0.29!7.97;;chr3:48282587..48282603,+!0.29!7.14;;chr7:99156212..99156244,+!0.29!6.06;;chr19:56915668..56915732,+!0.29!5.83;;chr10:43133950..43133994,-!0.29!5.59;;chr12:3069037..3069119,+!0.29!5.35;;chr19:37341752..37341816,+!0.29!4.64;;chr1:33721900..33721921,+!0.29!3.57;;chr19:56152332..56152347,+!0.29!3.21;;chr19:19932586..19932598,-!0.29!2.74;;chr11:67007445..67007459,+!0.29!2.26;;chr19:18391593..18391611,-!0.29!2.14;;chr20:49547554..49547563,-!0.29!2.02;;chr3:14989024..14989041,+!0.29!1.66;;chr15:37390482..37390572,-!0.29!1.66;;chr11:65688056..65688069,+!0.29!0.95;;chr12:26278030..26278039,-!0.29!0.95;;chr12:54394059..54394088,+!0.29!0.95;;chr12:54402790..54402805,+!0.29!0.95;;chr12:66218469..66218477,+!0.29!0.95;;chr13:112721457..112721482,+!0.29!0.95;;chr13:28543285..28543314,-!0.29!0.95;;chr19:22469215..22469229,+!0.29!0.95;;chr19:37464453..37464515,+!0.29!0.95;;chr19:38183166..38183184,-!0.29!0.95;;chr2:176987441..176987454,+!0.29!0.95;;chr2:45169172..45169177,+!0.29!0.95;;chr2:45169179..45169190,+!0.29!0.95;;chr2:45169317..45169326,+!0.29!0.95;;chr21:30671130..30671140,+!0.29!0.95;;chr21:38071430..38071456,+!0.29!0.95;;chr3:138665937..138665968,-!0.29!0.95;;chr4:8873716..8873738,-!0.29!0.95;;chr5:92918789..92918800,+!0.29!0.95;;chr6:10412640..10412655,-!0.29!0.95;;chr6:1612300..1612324,+!0.29!0.95;;chr7:27205175..27205184,-!0.29!0.95;;chr7:96634878..96634900,+!0.29!0.95;;chr7:96654026..96654061,-!0.29!0.95;;chr8:60031534..60031553,-!0.29!0.95;;chr1:161736102..161736123,+!0.28!45.31;;chr19:19302931..19302974,-!0.28!42.45;;chr1:78444778..78444800,-!0.28!29.49;;chr16:67876180..67876242,+!0.28!28.66;;chr1:151319710..151319774,-!0.28!16.53;;chr6:35310312..35310359,+!0.28!15.10;;chr1:41157266..41157314,+!0.28!13.91;;chr1:157108130..157108173,-!0.28!11.89;;chr6:33285505..33285529,-!0.28!11.06;;chr20:42295713..42295738,+!0.28!9.63;;chr16:31085514..31085576,-!0.28!6.54;;chr5:178157651..178157689,-!0.28!6.42;;chr6:35227282..35227330,+!0.28!5.59;;chr3:150126706..150126754,+!0.28!4.64;;chr6:44233297..44233330,-!0.28!3.81;;chr12:19671171..19671175,+!0.28!3.21;;chr11:62369383..62369399,-!0.28!3.09;;chr19:57078854..57078889,+!0.28!1.90;;chr15:57025823..57025832,-!0.28!1.78;;chr11:64764435..64764449,-!0.28!1.55;;chr16:30546275..30546297,-!0.28!1.55;;chr11:19262486..19262512,-!0.28!1.31;;chr8:80680078..80680101,-!0.28!1.07;;chr2:25565377..25565389,-!0.28!1.07;;chr19:58125580..58125639,+!0.27!26.16;;chr1:247095236..247095283,-!0.27!17.48;;chr19:57901208..57901280,+!0.27!12.72;;chr1:6685228..6685270,+!0.27!11.54;;chr19:22018966..22019001,-!0.27!9.16;;chr19:12267524..12267564,-!0.27!7.61;;chr12:57400261..57400344,-!0.27!7.25;;chr4:492909..492968,-!0.27!6.90;;chr19:58962974..58963001,+!0.27!6.78;;chr16:30569678..30569720,-!0.27!5.23;;chr19:53193790..53193821,-!0.27!4.40;;chr4:1873155..1873185,+!0.27!3.92;;chr15:50647347..50647366,-!0.27!3.57;;chr19:12203100..12203132,+!0.27!2.62;;chr19:19976714..19976729,+!0.27!2.38;;chr11:46299539..46299620,+!0.27!2.02;;chr1:41157326..41157337,+!0.27!1.78;;chrX:83757493..83757508,-!0.27!1.55;;chr18:56531584..56531646,+!0.27!1.43;;chr16:30569801..30569845,-!0.27!1.43;;chr12:115122005..115122016,-!0.27!1.19;;chr17:46622440..46622477,-!0.27!1.07;;chr18:3448314..3448333,+!0.27!1.07;;chr10:22292613..22292674,-!0.26!47.81;;chr2:27805880..27805967,+!0.26!22.12;;chr16:3451184..3451264,+!0.26!16.77;;chr19:52772832..52772861,+!0.26!15.94;;chr16:89284104..89284150,+!0.26!10.94;;chr1:14026671..14026705,+!0.26!9.39;;chr21:27107259..27107299,+!0.26!8.92;;chr15:50647370..50647405,-!0.26!8.21;;chr19:44952635..44952668,-!0.26!7.49;;chr19:53030906..53030952,+!0.26!5.47;;chr19:58331073..58331084,+!0.26!5.47;;chr10:97890024..97890064,+!0.26!3.69;;chr16:30597000..30597068,-!0.26!3.45;;chr9:32550839..32550962,-!0.26!3.33;;chr12:133707172..133707202,+!0.26!2.97;;chr19:52674898..52674931,-!0.26!2.85;;chr19:8578683..8578750,-!0.26!2.74;;chr12:133706820..133706881,-!0.26!2.62;;chr14:64970361..64970389,-!0.26!2.50;;chr11:85376097..85376108,-!0.26!2.26;;chr18:3448455..3448480,+!0.26!2.26;;chr9:102584159..102584174,+!0.26!2.14;;chr18:56530136..56530199,+!0.26!1.66;;chr4:146436110..146436135,+!0.26!1.55;;chr8:86089627..86089653,+!0.26!1.07;;chr6:41040905..41040916,+!0.26!0.83;;chr7:27135054..27135060,-!0.26!0.83;;chr7:27170274..27170308,-!0.26!0.83;;chr7:73038867..73038878,-!0.26!0.83;;chr7:96654133..96654150,-!0.26!0.83;;chr8:144512897..144512903,-!0.26!0.83;;chr8:42698383..42698394,-!0.26!0.83;;chr9:100615499..100615519,+!0.26!0.83;;chr9:16727880..16727894,-!0.26!0.83;;chr19:11750543..11750565,+!0.26!0.83;;chr19:49140658..49140667,-!0.26!0.83;;chr19:49140692..49140709,-!0.26!0.83;;chr2:10091783..10091811,+!0.26!0.83;;chr2:200322723..200322739,-!0.26!0.83;;chr2:45169024..45169033,+!0.26!0.83;;chr2:45169684..45169715,+!0.26!0.83;;chr22:22874610..22874616,-!0.26!0.83;;chr3:147111505..147111529,+!0.26!0.83;;chr3:25469815..25469866,+!0.26!0.83;;chr5:5068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|fonse_cell_line=FF:0100353,FF:0101120
|fonse_cell_line=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0101120
|fonse_cell_line_closure=FF:0100353,FF:0101120

Revision as of 17:24, 29 March 2012


Name:small cell lung carcinoma cell line:DMS 144
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
sexmale
age68
cell typeunclassifiable
cell lineDMS 144
companyATCC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-penis0.054
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-lymphoma0.353
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs12808

Jaspar motifP-value
MA0002.20.00314
MA0003.10.189
MA0004.10.206
MA0006.10.229
MA0007.10.856
MA0009.10.841
MA0014.10.748
MA0017.10.00299
MA0018.20.128
MA0019.10.651
MA0024.13.09751e-4
MA0025.10.237
MA0027.10.578
MA0028.10.00968
MA0029.10.463
MA0030.10.192
MA0031.10.162
MA0035.20.602
MA0038.10.00261
MA0039.20.433
MA0040.10.4
MA0041.10.0943
MA0042.10.0815
MA0043.10.696
MA0046.10.129
MA0047.20.0982
MA0048.10.175
MA0050.13.14561e-12
MA0051.16.66465e-7
MA0052.10.0468
MA0055.10.0101
MA0057.10.0931
MA0058.10.169
MA0059.10.504
MA0060.14.54166e-14
MA0061.10.0227
MA0062.20.00819
MA0065.20.117
MA0066.10.238
MA0067.10.311
MA0068.10.523
MA0069.10.609
MA0070.10.0193
MA0071.10.915
MA0072.10.953
MA0073.10.43
MA0074.10.247
MA0076.11.39887e-4
MA0077.10.48
MA0078.10.483
MA0079.20.254
MA0080.23.52572e-13
MA0081.10.0344
MA0083.10.479
MA0084.10.978
MA0087.10.734
MA0088.10.0273
MA0090.10.257
MA0091.10.0432
MA0092.10.261
MA0093.10.134
MA0099.22.52898e-21
MA0100.10.1
MA0101.10.0608
MA0102.24.88478e-5
MA0103.10.459
MA0104.20.073
MA0105.10.0518
MA0106.10.515
MA0107.10.0162
MA0108.20.34
MA0111.10.862
MA0112.20.00122
MA0113.10.0234
MA0114.10.12
MA0115.10.904
MA0116.10.0892
MA0117.10.855
MA0119.10.31
MA0122.10.531
MA0124.10.946
MA0125.10.187
MA0131.10.143
MA0135.10.181
MA0136.12.28982e-10
MA0137.20.0308
MA0138.20.476
MA0139.10.159
MA0140.10.964
MA0141.10.279
MA0142.10.973
MA0143.10.75
MA0144.15.80317e-4
MA0145.10.109
MA0146.10.379
MA0147.10.082
MA0148.10.068
MA0149.10.909
MA0150.13.39755e-5
MA0152.10.787
MA0153.10.0978
MA0154.10.0256
MA0155.10.296
MA0156.10.00131
MA0157.10.397
MA0159.10.0552
MA0160.10.278
MA0162.10.224
MA0163.10.0861
MA0164.10.666
MA0258.10.0172
MA0259.10.0472



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: CNhs12808

Novel motifP-value
10.827
100.888
1000.322
1010.848
1020.472
1030.231
1040.577
1050.279
1066.70058e-7
1070.00169
1080.57
1090.57
110.481
1100.797
1110.784
1120.0396
1130.468
1140.364
1150.685
1160.856
1170.941
1180.994
1190.363
120.728
1200.554
1210.23
1220.641
1230.635
1240.629
1250.00667
1260.137
1270.65
1280.00205
1290.3
130.929
1300.514
1310.0185
1320.248
1330.14
1340.953
1350.0152
1360.457
1370.182
1380.209
1390.0465
140.55
1400.903
1410.571
1420.506
1430.21
1440.688
1450.549
1460.265
1470.553
1480.0157
1490.109
150.559
1500.256
1510.258
1520.0118
1530.237
1540.672
1550.532
1560.976
1570.959
1580.535
1590.265
160.308
1600.442
1610.792
1620.318
1630.31
1640.909
1650.231
1660.262
1670.176
1680.0996
1690.0335
170.155
180.338
190.157
20.0485
200.417
210.575
220.229
231.25933e-4
240.918
250.689
260.321
270.161
280.756
290.377
30.462
300.188
310.722
320.0481
330.969
340.278
350.942
360.583
370.331
380.323
390.195
40.285
400.747
410.129
420.82
430.335
440.661
450.179
460.337
470.802
480.644
490.504
50.219
500.598
510.82
520.0127
530.319
540.359
550.814
560.47
570.911
580.256
590.0393
60.669
600.0026
610.925
620.136
630.317
640.753
650.0419
660.0363
670.426
680.098
690.768
70.72
700.207
710.206
720.218
730.0938
740.528
750.702
760.629
770.114
780.221
790.135
80.79
800.014
810.696
820.404
830.386
840.956
850.00824
860.534
870.948
880.956
890.0314
90.116
900.805
910.0783
920.208
930.935
940.18
950.405
960.459
970.898
980.687
990.72



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: CNhs12808


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050615 (respiratory system cancer)
0050686 (organ system cancer)
0050687 (cell type cancer)
1324 (lung cancer)
1325 (bronchus cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
3904 (bronchogenic carcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial 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)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002048 (lung)
0002050 (embryonic structure)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0007026 (primitive gut)
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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