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FF:10019-101D1: 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 16:26, 29 March 2012


Name:lung, adult, pool1
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 stage46,65,94 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -10
catalog numberCat:AM6000 Lot:0910061 -10
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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-0.113
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0441
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.199
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.0441
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0.731
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0.121
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: CNhs10625

Jaspar motifP-value
MA0002.20.647
MA0003.10.123
MA0004.10.121
MA0006.10.119
MA0007.10.253
MA0009.10.115
MA0014.10.988
MA0017.10.799
MA0018.20.87
MA0019.10.0234
MA0024.10.0494
MA0025.10.0874
MA0027.10.629
MA0028.11.65541e-8
MA0029.10.247
MA0030.12.55577e-6
MA0031.11.67065e-4
MA0035.20.797
MA0038.10.929
MA0039.20.0575
MA0040.10.31
MA0041.10.0854
MA0042.10.124
MA0043.10.619
MA0046.10.00112
MA0047.21.73008e-7
MA0048.10.00892
MA0050.18.53737e-7
MA0051.16.92266e-4
MA0052.14.67961e-4
MA0055.19.80005e-4
MA0057.10.817
MA0058.10.0798
MA0059.10.0119
MA0060.10.169
MA0061.10.356
MA0062.21.83256e-8
MA0065.20.226
MA0066.10.149
MA0067.10.719
MA0068.12.8024e-4
MA0069.10.681
MA0070.10.293
MA0071.10.0548
MA0072.10.194
MA0073.10.958
MA0074.10.936
MA0076.16.54783e-10
MA0077.10.899
MA0078.10.168
MA0079.20.0645
MA0080.26.61508e-7
MA0081.10.28
MA0083.10.00395
MA0084.10.771
MA0087.10.138
MA0088.18.23498e-4
MA0090.10.0743
MA0091.10.838
MA0092.10.954
MA0093.10.105
MA0099.21.65037e-6
MA0100.10.812
MA0101.10.871
MA0102.20.00168
MA0103.10.268
MA0104.20.00118
MA0105.10.00825
MA0106.10.0375
MA0107.10.973
MA0108.21.08349e-16
MA0111.10.616
MA0112.20.813
MA0113.10.186
MA0114.10.149
MA0115.10.565
MA0116.10.0395
MA0117.10.304
MA0119.10.67
MA0122.10.0993
MA0124.10.84
MA0125.10.904
MA0131.10.117
MA0135.10.692
MA0136.19.76517e-4
MA0137.21.38105e-4
MA0138.20.54
MA0139.10.541
MA0140.10.983
MA0141.10.0542
MA0142.10.359
MA0143.10.437
MA0144.10.0026
MA0145.10.0225
MA0146.10.532
MA0147.11.85274e-4
MA0148.18.25543e-6
MA0149.10.115
MA0150.10.0783
MA0152.10.959
MA0153.15.57892e-7
MA0154.10.986
MA0155.10.526
MA0156.10.202
MA0157.10.0164
MA0159.10.803
MA0160.10.385
MA0162.10.929
MA0163.15.86178e-6
MA0164.10.0827
MA0258.10.232
MA0259.10.0102



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: CNhs10625

Novel motifP-value
10.0917
100.0122
1000.189
1010.658
1020.838
1030.449
1040.975
1050.417
1060.16
1070.0393
1080.92
1090.239
110.236
1100.313
1110.0858
1120.711
1130.834
1140.0381
1150.248
1160.158
1170.0293
1180.0386
1190.208
120.611
1200.0339
1210.471
1220.655
1230.0135
1240.816
1250.165
1260.192
1270.935
1280.33
1290.0187
130.338
1300.424
1310.0548
1320.456
1330.0548
1340.237
1350.0286
1360.776
1370.256
1380.998
1390.336
140.727
1400.0552
1410.23
1420.373
1430.413
1440.589
1450.553
1460.243
1470.808
1480.444
1490.332
150.421
1500.863
1510.873
1520.0344
1530.642
1540.479
1550.385
1560.994
1570.591
1580.527
1590.852
160.951
1600.941
1610.348
1620.983
1630.701
1640.0169
1650.0131
1660.587
1670.00482
1680.15
1690.693
170.958
180.0805
190.37
20.0707
200.127
210.454
220.593
230.0823
240.618
250.466
260.393
270.635
280.889
290.0289
30.276
300.0237
310.999
320.68
330.517
340.168
350.203
360.0759
370.441
380.941
390.11
40.0958
400.452
410.518
420.366
430.685
440.861
450.0971
460.306
470.176
480.245
490.211
50.838
500.569
510.812
520.0428
530.697
540.908
550.47
560.99
570.0347
580.798
590.343
60.483
600.19
610.694
620.587
630.997
640.287
650.745
660.0449
670.753
680.567
690.852
70.861
700.0642
710.109
720.282
730.974
740.761
750.00565
760.0402
770.177
780.294
790.891
80.47
800.0178
810.541
820.689
830.284
840.862
850.343
860.639
870.741
880.944
890.734
90.165
900.0534
910.738
920.705
930.0492
940.192
950.286
960.755
970.593
980.155
990.855



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: CNhs10625


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

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)
0007023 (adult organism)
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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