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FF:10047-101G2: 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 16:30, 29 March 2012


Name:tonsil, 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
tissuetonsil
dev stage22-61 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number9120165A
catalog numberCat:636587
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-Basophils0.0549
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0742
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-lymphoma0.0375
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0.0283
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.0283
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-Whole0.126
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: CNhs10654

Jaspar motifP-value
MA0002.20.00295
MA0003.10.217
MA0004.10.367
MA0006.10.213
MA0007.10.396
MA0009.10.218
MA0014.10.452
MA0017.10.21
MA0018.20.262
MA0019.10.302
MA0024.10.96
MA0025.10.49
MA0027.10.917
MA0028.10.215
MA0029.10.618
MA0030.10.0213
MA0031.10.175
MA0035.20.885
MA0038.10.558
MA0039.20.00284
MA0040.10.522
MA0041.10.0731
MA0042.10.402
MA0043.10.133
MA0046.10.997
MA0047.20.0351
MA0048.18.54712e-4
MA0050.12.13983e-6
MA0051.10.0214
MA0052.11.74234e-8
MA0055.10.0189
MA0057.10.27
MA0058.10.244
MA0059.10.0311
MA0060.10.182
MA0061.10.64
MA0062.20.294
MA0065.20.91
MA0066.10.615
MA0067.10.143
MA0068.10.172
MA0069.10.406
MA0070.10.931
MA0071.10.0412
MA0072.10.571
MA0073.10.914
MA0074.10.39
MA0076.10.831
MA0077.10.768
MA0078.10.313
MA0079.20.0221
MA0080.21.64911e-11
MA0081.10.0675
MA0083.10.186
MA0084.10.664
MA0087.10.147
MA0088.10.209
MA0090.10.283
MA0091.10.532
MA0092.10.946
MA0093.10.39
MA0099.22.90643e-6
MA0100.10.294
MA0101.10.886
MA0102.20.597
MA0103.14.66511e-5
MA0104.20.0466
MA0105.10.0927
MA0106.10.974
MA0107.10.76
MA0108.24.61026e-23
MA0111.10.737
MA0112.20.339
MA0113.10.233
MA0114.10.846
MA0115.10.854
MA0116.10.894
MA0117.10.333
MA0119.10.244
MA0122.10.0763
MA0124.10.378
MA0125.10.747
MA0131.10.391
MA0135.10.0489
MA0136.12.32695e-14
MA0137.20.234
MA0138.20.679
MA0139.10.687
MA0140.10.566
MA0141.10.038
MA0142.10.993
MA0143.10.294
MA0144.10.296
MA0145.10.0177
MA0146.10.176
MA0147.10.0284
MA0148.10.405
MA0149.10.362
MA0150.10.00469
MA0152.10.102
MA0153.10.799
MA0154.10.125
MA0155.10.559
MA0156.18.2479e-10
MA0157.10.434
MA0159.10.829
MA0160.10.361
MA0162.10.842
MA0163.10.0248
MA0164.10.418
MA0258.10.973
MA0259.10.0983



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: CNhs10654

Novel motifP-value
10.497
100.0428
1000.0947
1010.913
1020.634
1030.649
1040.698
1050.0909
1060.365
1070.161
1080.811
1090.972
110.841
1100.617
1110.333
1120.201
1130.0548
1140.156
1150.596
1160.0973
1170.339
1180.0338
1190.724
120.595
1200.17
1210.0595
1220.177
1230.368
1240.515
1250.907
1260.146
1270.257
1280.612
1290.861
130.272
1300.375
1310.587
1320.261
1334.73588e-4
1340.00157
1350.0246
1360.964
1370.249
1380.968
1390.551
140.425
1400.561
1410.324
1420.596
1430.947
1440.0518
1450.415
1460.0133
1470.826
1480.841
1490.0871
150.236
1500.89
1510.507
1520.109
1530.324
1540.56
1550.618
1560.916
1570.204
1580.969
1590.615
160.833
1600.673
1610.88
1620.698
1630.447
1640.0243
1650.697
1660.914
1670.0446
1682.72809e-4
1690.168
170.719
180.108
190.675
20.028
200.12
210.726
220.327
230.452
240.781
250.477
260.717
270.144
280.843
290.232
30.872
300.0207
310.947
320.0747
330.689
340.322
350.23
360.0989
370.625
380.579
390.911
40.958
400.878
410.754
420.933
430.968
440.903
450.0178
460.795
470.75
480.944
490.826
50.811
500.345
510.966
520.238
530.286
540.849
550.639
560.76
570.294
580.483
590.336
60.309
600.303
610.707
620.837
630.487
640.955
650.526
660.528
670.47
680.724
690.901
70.522
700.239
710.273
720.0609
730.762
740.105
750.342
760.0628
770.226
780.617
790.145
80.604
807.56823e-5
810.771
820.9
830.728
840.111
850.945
860.788
870.56
880.812
890.666
90.173
900.0755
910.412
920.47
930.999
940.341
950.802
960.909
970.54
980.31
990.382



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: CNhs10654


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
0000033 (head)
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)
0000153 (anterior region of body)
0000161 (orifice)
0000165 (mouth)
0000166 (oral opening)
0000344 (mucosa)
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)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000930 (stomodeum)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0001735 (tonsillar ring)
0001744 (lymphoid tissue)
0001961 (mucosa-associated lymphoid tissue)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002372 (tonsil)
0002405 (immune system)
0002465 (lymphoid system)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0006562 (pharynx)
0007023 (adult organism)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

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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