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FF:10195-103E6: 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 17:23, 29 March 2012


Name:olfactory region, adult
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueolfactory apparatus
dev stageNA
sexfemale
age87
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberR1234063-10
sample typeNA
extraction protocol (Details)NA
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-Neural0.39
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-penis0.52
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-0.314
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.065
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0.216
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs12611

Jaspar motifP-value
MA0002.20.0327
MA0003.10.299
MA0004.10.332
MA0006.10.282
MA0007.10.205
MA0009.10.155
MA0014.10.565
MA0017.10.00183
MA0018.20.391
MA0019.10.774
MA0024.10.912
MA0025.10.67
MA0027.10.647
MA0028.10.0364
MA0029.10.0135
MA0030.10.74
MA0031.10.523
MA0035.20.00779
MA0038.10.496
MA0039.20.0913
MA0040.10.887
MA0041.10.78
MA0042.10.952
MA0043.10.513
MA0046.10.00206
MA0047.20.0242
MA0048.10.111
MA0050.10.0178
MA0051.10.0851
MA0052.10.771
MA0055.10.00109
MA0057.11
MA0058.10.264
MA0059.10.0844
MA0060.10.882
MA0061.10.00564
MA0062.20.00129
MA0065.26.53584e-4
MA0066.10.0159
MA0067.10.966
MA0068.10.56
MA0069.10.488
MA0070.10.674
MA0071.10.0221
MA0072.10.174
MA0073.10.426
MA0074.10.217
MA0076.10.071
MA0077.10.31
MA0078.10.858
MA0079.20.633
MA0080.22.50156e-9
MA0081.10.0254
MA0083.10.025
MA0084.10.777
MA0087.10.755
MA0088.10.156
MA0090.10.303
MA0091.10.586
MA0092.10.429
MA0093.10.327
MA0099.23.45179e-20
MA0100.10.551
MA0101.17.31694e-4
MA0102.20.0483
MA0103.10.23
MA0104.20.403
MA0105.10.00161
MA0106.10.0228
MA0107.10.00149
MA0108.20.254
MA0111.10.549
MA0112.20.00108
MA0113.10.286
MA0114.10.00239
MA0115.10.742
MA0116.10.00696
MA0117.10.894
MA0119.10.0839
MA0122.10.6
MA0124.10.596
MA0125.10.351
MA0131.10.852
MA0135.10.0665
MA0136.11.47971e-14
MA0137.20.252
MA0138.20.204
MA0139.10.407
MA0140.12.89402e-4
MA0141.10.00705
MA0142.10.965
MA0143.10.523
MA0144.10.213
MA0145.10.172
MA0146.10.012
MA0147.10.288
MA0148.10.0492
MA0149.10.017
MA0150.17.09415e-5
MA0152.10.651
MA0153.10.128
MA0154.10.048
MA0155.10.643
MA0156.11.53101e-9
MA0157.10.317
MA0159.10.00568
MA0160.10.0097
MA0162.10.14
MA0163.12.4137e-5
MA0164.10.827
MA0258.10.0124
MA0259.10.81



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: CNhs12611

Novel motifP-value
10.0512
100.0448
1000.309
1010.416
1020.751
1030.209
1040.156
1050.117
1060.0453
1070.13
1080.905
1090.00273
110.0127
1100.0495
1110.152
1120.51
1130.395
1140.212
1150.918
1160.233
1170.00954
1180.151
1190.227
120.472
1200.253
1210.291
1220.922
1230.788
1240.0747
1250.2
1260.0223
1270.598
1280.241
1290.574
137.90152e-4
1300.16
1310.121
1320.59
1330.0329
1340.511
1350.172
1360.002
1370.751
1380.876
1390.19
140.785
1400.653
1410.649
1420.952
1430.0683
1440.949
1450.103
1460.415
1470.767
1480.299
1490.336
150.0598
1500.142
1510.617
1520.0765
1530.909
1540.46
1550.748
1560.332
1570.437
1580.206
1590.0126
160.0537
1600.285
1610.286
1620.7
1630.745
1640.0394
1650.0379
1660.914
1670.821
1680.542
1690.0107
170.154
180.171
190.186
20.95
200.106
210.0947
220.214
230.425
240.0356
250.44
261.23383e-4
270.919
280.639
290.00978
30.0333
300.805
310.963
320.0565
330.0418
340.648
350.61
360.137
370.027
380.326
390.204
40.744
400.0261
410.337
420.18
430.105
440.317
450.686
460.083
470.0676
480.0555
490.194
50.534
500.293
510.497
520.586
530.909
540.414
550.613
560.451
570.324
580.307
590.108
60.778
600.0657
610.0605
620.197
630.174
640.217
650.268
660.114
670.321
680.177
690.529
70.0439
700.0497
710.00961
720.345
730.0228
740.85
750.0287
760.398
770.2
780.00159
790.482
80.0756
800.545
810.722
820.604
830.0384
840.546
850.264
860.167
871.31517e-4
880.839
890.616
90.378
900.112
910.781
920.604
930.951
940.156
950.0091
960.974
970.682
980.307
990.66



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: CNhs12611


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)
0000075 (subdivision of skeletal system)
0000153 (anterior region of body)
0000465 (material 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)
0000924 (ectoderm)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001703 (neurocranium)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002241 (chondrocranium)
0002329 (somite)
0002342 (neural crest)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003075 (neural plate)
0003077 (paraxial mesoderm)
0003089 (sclerotome)
0003104 (mesenchyme)
0003112 (olfactory region)
0003128 (cranium)
0003129 (skull)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004288 (skeleton)
0004765 (skeletal element)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007284 (presumptive neural plate)
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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