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FF:11563-120D6: 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 17:22, 29 March 2012


Name:Mast cell, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stage76 years old adult
sexfemale
age76
cell typemast cell
cell lineNA
companyNA
collaborationSven Guhl (Charite Germany)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberBsMC-Q
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-0.0421
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-lymphoma0.131
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
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: CNhs12566

Jaspar motifP-value
MA0002.22.67082e-6
MA0003.10.529
MA0004.10.421
MA0006.10.774
MA0007.10.298
MA0009.10.0817
MA0014.10.841
MA0017.10.163
MA0018.20.106
MA0019.10.691
MA0024.10.247
MA0025.10.267
MA0027.10.83
MA0028.12.42265e-6
MA0029.17.05809e-4
MA0030.10.927
MA0031.10.552
MA0035.21.90822e-15
MA0038.16.30351e-4
MA0039.20.849
MA0040.10.45
MA0041.10.375
MA0042.10.186
MA0043.10.00327
MA0046.10.263
MA0047.20.647
MA0048.10.112
MA0050.14.56198e-5
MA0051.10.0526
MA0052.10.0547
MA0055.10.517
MA0057.10.918
MA0058.10.649
MA0059.10.543
MA0060.10.0299
MA0061.10.55
MA0062.24.4677e-19
MA0065.20.439
MA0066.10.459
MA0067.10.0146
MA0068.10.0298
MA0069.10.872
MA0070.10.0158
MA0071.10.185
MA0072.10.825
MA0073.10.218
MA0074.10.663
MA0076.12.53207e-8
MA0077.10.403
MA0078.10.379
MA0079.20.0482
MA0080.22.29256e-12
MA0081.14.44253e-4
MA0083.17.845e-4
MA0084.10.574
MA0087.10.496
MA0088.10.966
MA0090.14.66919e-6
MA0091.10.236
MA0092.10.815
MA0093.10.677
MA0099.20.125
MA0100.10.0379
MA0101.10.674
MA0102.20.47
MA0103.10.705
MA0104.20.51
MA0105.10.15
MA0106.10.263
MA0107.10.235
MA0108.29.72514e-12
MA0111.10.211
MA0112.20.229
MA0113.10.933
MA0114.10.262
MA0115.10.00473
MA0116.10.0451
MA0117.10.733
MA0119.10.138
MA0122.10.439
MA0124.10.302
MA0125.10.77
MA0131.10.404
MA0135.10.616
MA0136.13.78401e-13
MA0137.20.527
MA0138.20.903
MA0139.10.0823
MA0140.11.30986e-11
MA0141.10.0575
MA0142.10.904
MA0143.10.795
MA0144.10.59
MA0145.10.566
MA0146.10.0037
MA0147.10.348
MA0148.10.29
MA0149.10.322
MA0150.10.715
MA0152.10.121
MA0153.10.0762
MA0154.10.227
MA0155.10.905
MA0156.13.34579e-13
MA0157.10.596
MA0159.10.013
MA0160.10.00556
MA0162.10.00112
MA0163.10.00866
MA0164.10.397
MA0258.10.0675
MA0259.10.404



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: CNhs12566

Novel motifP-value
10.714
100.0581
1000.301
1010.349
1020.0725
1030.11
1040.806
1050.789
1060.611
1070.488
1080.0961
1090.00516
110.287
1100.599
1110.231
1120.0922
1130.0782
1140.0386
1150.845
1160.628
1170.00309
1180.285
1190.895
120.583
1200.768
1210.214
1220.401
1230.182
1240.848
1250.611
1260.458
1270.345
1280.769
1290.304
130.775
1300.255
1310.62
1320.705
1330.835
1340.285
1350.0323
1360.0672
1370.0761
1380.19
1390.477
140.27
1400.272
1410.299
1420.419
1430.588
1440.121
1450.288
1460.857
1470.0671
1480.542
1490.398
150.129
1500.184
1510.44
1520.673
1530.115
1540.785
1550.0103
1560.921
1570.802
1580.164
1590.986
160.623
1600.141
1610.797
1620.937
1630.99
1640.337
1650.511
1660.00982
1670.588
1680.46
1690.881
170.919
180.405
190.789
20.383
200.572
210.0173
220.213
230.408
240.0821
250.32
260.481
270.395
280.199
290.154
30.649
300.137
310.803
320.0863
330.644
340.958
350.749
360.555
370.165
380.367
390.348
40.868
400.228
410.951
420.618
430.741
440.652
450.976
460.604
470.299
480.345
490.7
50.885
500.483
510.341
520.432
530.489
540.365
550.887
560.563
570.985
580.017
590.628
60.619
600.958
610.0999
620.047
630.605
640.724
650.939
660.276
670.743
680.339
690.693
70.577
700.729
710.335
720.0354
730.198
740.121
750.113
760.821
770.224
780.00907
790.806
80.972
800.707
810.68
820.582
830.839
840.923
850.711
860.193
870.0833
880.211
890.247
90.891
900.161
910.995
920.791
930.299
940.198
959.01286e-5
960.415
970.485
980.495
990.336



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: CNhs12566


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000097 (mast cell)
0000134 (mesenchymal cell)
0000151 (secretory cell)
0000163 (endocrine cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000457 (biogenic amine secreting cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000831 (mast cell progenitor)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002028 (basophil mast progenitor cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002191 (granulocytopoietic cell)
0002274 (histamine secreting cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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