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FF:10189-103D9: 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 17:25, 29 March 2012


Name:appendix, adult
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sex29
ageM
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberR1234006-10
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
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-0.124
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-lymphoma0.144
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0.106
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: CNhs12842

Jaspar motifP-value
MA0002.20.332
MA0003.10.178
MA0004.10.121
MA0006.10.309
MA0007.10.549
MA0009.10.896
MA0014.10.317
MA0017.10.175
MA0018.20.998
MA0019.10.314
MA0024.10.106
MA0025.10.865
MA0027.10.402
MA0028.10.195
MA0029.10.184
MA0030.10.00382
MA0031.10.0777
MA0035.20.415
MA0038.10.374
MA0039.20.188
MA0040.10.946
MA0041.10.908
MA0042.10.565
MA0043.10.409
MA0046.13.65488e-10
MA0047.20.0572
MA0048.10.0308
MA0050.19.52587e-11
MA0051.18.22093e-6
MA0052.10.0703
MA0055.16.57389e-4
MA0057.10.966
MA0058.10.0563
MA0059.10.00115
MA0060.10.539
MA0061.10.418
MA0062.20.715
MA0065.20.166
MA0066.10.00127
MA0067.10.278
MA0068.17.14068e-5
MA0069.10.366
MA0070.10.184
MA0071.10.0283
MA0072.10.151
MA0073.10.826
MA0074.10.293
MA0076.10.791
MA0077.10.72
MA0078.10.0775
MA0079.20.0456
MA0080.26.37867e-10
MA0081.10.025
MA0083.10.00117
MA0084.10.274
MA0087.10.349
MA0088.10.0881
MA0090.10.141
MA0091.10.295
MA0092.10.757
MA0093.10.121
MA0099.23.10524e-17
MA0100.10.282
MA0101.10.968
MA0102.20.214
MA0103.10.0544
MA0104.20.00119
MA0105.19.66562e-5
MA0106.10.00181
MA0107.10.748
MA0108.27.99201e-12
MA0111.10.977
MA0112.20.0115
MA0113.10.422
MA0114.10.978
MA0115.10.602
MA0116.10.00769
MA0117.10.187
MA0119.10.0253
MA0122.10.248
MA0124.10.642
MA0125.10.299
MA0131.10.78
MA0135.10.0525
MA0136.12.66906e-9
MA0137.20.0444
MA0138.20.603
MA0139.10.0747
MA0140.10.0629
MA0141.10.00356
MA0142.10.757
MA0143.10.245
MA0144.10.526
MA0145.10.753
MA0146.10.39
MA0147.14.50961e-4
MA0148.10.51
MA0149.10.0741
MA0150.11.37824e-7
MA0152.10.457
MA0153.15.96661e-7
MA0154.10.14
MA0155.10.916
MA0156.12.5227e-6
MA0157.10.768
MA0159.10.0797
MA0160.10.0349
MA0162.10.45
MA0163.12.9967e-8
MA0164.10.289
MA0258.10.0225
MA0259.10.0137



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: CNhs12842

Novel motifP-value
10.0164
100.088
1000.1
1010.853
1020.504
1030.12
1040.986
1050.499
1060.563
1070.768
1080.947
1090.0525
110.111
1100.0969
1110.215
1120.994
1130.232
1140.00105
1150.837
1160.21
1170.0932
1180.0601
1190.865
120.947
1200.238
1210.514
1220.707
1230.903
1240.885
1250.15
1260.48
1270.587
1280.878
1290.0772
130.0634
1300.629
1310.618
1320.173
1330.00393
1340.0841
1350.12
1360.936
1370.913
1380.931
1390.137
140.707
1400.275
1410.276
1420.641
1430.344
1440.897
1450.944
1460.683
1470.575
1480.516
1490.977
150.0359
1500.321
1510.365
1520.972
1530.881
1540.606
1550.73
1560.298
1570.0436
1580.14
1590.473
160.0551
1600.325
1610.878
1620.912
1630.51
1640.0301
1650.751
1660.276
1670.0444
1680.0019
1690.11
170.473
180.0191
190.66
20.1
200.0704
210.311
220.586
230.944
240.572
250.99
260.298
270.392
280.903
290.0301
30.357
300.0954
310.63
320.135
330.152
340.34
350.105
360.0395
370.0269
380.737
390.76
40.347
400.101
410.18
420.415
430.119
440.536
450.357
460.0882
470.113
480.132
490.131
50.263
500.662
510.905
520.451
530.393
540.982
550.6
560.693
570.109
580.774
590.786
60.385
600.944
610.951
620.542
630.355
640.194
650.603
660.0815
670.225
680.81
690.146
70.66
700.0172
710.0308
720.369
730.18
740.883
750.0371
760.216
770.588
780.46
790.0533
80.147
800.0196
810.87
820.292
830.238
840.00636
850.185
860.962
870.936
880.657
890.408
90.36
900.122
910.451
920.622
930.221
940.0573
950.0518
960.716
970.418
980.0987
990.7



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: CNhs12842


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
0000059 (large intestine)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001007 (digestive system)
0001045 (midgut)
0001062 (anatomical entity)
0001153 (caecum)
0001154 (vermiform appendix)
0001155 (colon)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007026 (primitive gut)
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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