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FF:10068-101I5: 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 16:48, 29 March 2012


Name:lung, fetal, 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 stage40 weeks fetus
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA506331
catalog numberCat:RtHFN: Lung
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-0.213
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
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
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0.383
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: CNhs11680

Jaspar motifP-value
MA0002.20.0462
MA0003.10.592
MA0004.10.0413
MA0006.10.812
MA0007.10.332
MA0009.10.623
MA0014.10.422
MA0017.10.115
MA0018.20.159
MA0019.10.211
MA0024.10.736
MA0025.10.391
MA0027.10.83
MA0028.10.00987
MA0029.10.322
MA0030.11.88072e-8
MA0031.15.11856e-5
MA0035.20.157
MA0038.10.804
MA0039.20.319
MA0040.10.0796
MA0041.10.19
MA0042.10.152
MA0043.10.109
MA0046.10.012
MA0047.24.57708e-7
MA0048.10.0706
MA0050.10.552
MA0051.10.471
MA0052.11.58971e-5
MA0055.10.00488
MA0057.10.545
MA0058.10.0215
MA0059.10.00189
MA0060.10.263
MA0061.10.114
MA0062.20.0016
MA0065.25.46557e-4
MA0066.10.00885
MA0067.10.312
MA0068.10.00757
MA0069.10.868
MA0070.10.296
MA0071.10.0108
MA0072.10.295
MA0073.10.44
MA0074.10.354
MA0076.10.0437
MA0077.10.971
MA0078.10.25
MA0079.20.411
MA0080.20.396
MA0081.10.617
MA0083.10.0843
MA0084.10.958
MA0087.10.0908
MA0088.10.038
MA0090.10.137
MA0091.10.558
MA0092.10.241
MA0093.10.0438
MA0099.21.04899e-10
MA0100.10.375
MA0101.10.576
MA0102.20.131
MA0103.10.323
MA0104.20.00597
MA0105.18.62271e-4
MA0106.10.0445
MA0107.10.673
MA0108.21.42003e-7
MA0111.10.897
MA0112.20.00207
MA0113.10.572
MA0114.10.0038
MA0115.10.197
MA0116.10.00443
MA0117.10.432
MA0119.10.547
MA0122.10.231
MA0124.10.874
MA0125.10.249
MA0131.10.947
MA0135.10.524
MA0136.10.798
MA0137.29.58227e-5
MA0138.20.368
MA0139.10.382
MA0140.10.0631
MA0141.10.00164
MA0142.10.0604
MA0143.10.379
MA0144.10.0529
MA0145.10.661
MA0146.10.0285
MA0147.10.00255
MA0148.12.63519e-6
MA0149.10.0187
MA0150.12.65555e-4
MA0152.10.436
MA0153.14.57741e-7
MA0154.10.145
MA0155.10.984
MA0156.10.728
MA0157.10.0454
MA0159.10.147
MA0160.10.0103
MA0162.10.234
MA0163.13.46679e-8
MA0164.10.303
MA0258.10.00696
MA0259.10.135



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: CNhs11680

Novel motifP-value
10.0111
100.0193
1000.247
1010.753
1020.407
1030.385
1040.796
1050.596
1060.182
1070.695
1080.262
1090.00595
110.0282
1100.132
1110.00337
1120.703
1130.381
1140.0194
1150.894
1160.135
1170.00628
1180.103
1190.056
120.893
1200.103
1210.467
1220.992
1230.0435
1240.904
1250.0366
1260.936
1270.118
1280.279
1290.165
130.305
1300.568
1310.0547
1320.604
1330.162
1340.677
1350.108
1360.134
1370.904
1380.495
1390.0277
140.944
1400.4
1410.394
1420.433
1430.0146
1440.687
1450.584
1460.926
1470.694
1480.0266
1490.643
150.258
1500.237
1510.434
1520.171
1530.685
1540.649
1550.135
1560.424
1570.801
1580.683
1590.285
160.116
1600.643
1610.332
1620.663
1630.7
1640.0574
1650.415
1660.714
1670.00721
1680.718
1690.00367
170.202
180.0174
190.73
20.504
200.231
210.255
220.47
230.662
240.874
250.523
260.0132
270.496
280.97
290.0315
30.114
300.154
310.594
320.367
330.513
340.615
350.165
360.0247
370.0542
380.497
390.448
40.318
400.0727
410.274
420.411
430.142
440.164
450.504
460.0608
470.0447
480.0596
490.0515
50.753
500.907
510.665
520.557
530.693
540.661
550.665
560.568
570.138
580.635
590.458
60.475
600.858
610.189
620.368
630.308
640.0714
650.39
660.0993
670.584
680.566
690.169
70.743
700.0147
710.0694
720.64
730.0219
740.268
750.00514
760.135
770.573
780.0273
790.266
80.0525
800.162
810.0863
820.241
830.914
840.531
850.322
860.533
878.6695e-4
880.824
890.376
90.769
900.0506
910.98
920.616
930.141
940.071
950.00672
960.287
970.501
980.111
990.456



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: CNhs11680


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)
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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