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FF:11487-119E2: 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 16:38, 29 March 2012


Name:Mast cell - stimulated, 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 numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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
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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
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: CNhs11073

Jaspar motifP-value
MA0002.26.46734e-4
MA0003.10.89
MA0004.10.0476
MA0006.10.642
MA0007.10.058
MA0009.10.38
MA0014.10.958
MA0017.10.24
MA0018.29.07425e-5
MA0019.10.0744
MA0024.10.815
MA0025.10.529
MA0027.10.794
MA0028.15.92924e-7
MA0029.10.0565
MA0030.10.247
MA0031.10.294
MA0035.27.37751e-8
MA0038.10.0127
MA0039.20.198
MA0040.10.22
MA0041.10.121
MA0042.10.49
MA0043.10.0121
MA0046.10.407
MA0047.20.196
MA0048.10.749
MA0050.10.0122
MA0051.10.104
MA0052.10.52
MA0055.10.0804
MA0057.10.679
MA0058.10.114
MA0059.10.995
MA0060.10.433
MA0061.10.154
MA0062.21.45684e-16
MA0065.20.421
MA0066.10.562
MA0067.10.0011
MA0068.10.121
MA0069.10.657
MA0070.10.00289
MA0071.10.57
MA0072.10.549
MA0073.10.399
MA0074.10.781
MA0076.12.82172e-9
MA0077.10.171
MA0078.10.87
MA0079.20.629
MA0080.23.6627e-9
MA0081.11.14301e-4
MA0083.10.599
MA0084.10.724
MA0087.10.97
MA0088.10.608
MA0090.14.24263e-4
MA0091.10.558
MA0092.10.496
MA0093.10.0811
MA0099.21.45921e-4
MA0100.10.156
MA0101.10.0525
MA0102.20.792
MA0103.10.0097
MA0104.20.565
MA0105.10.00714
MA0106.10.0591
MA0107.10.132
MA0108.20.013
MA0111.10.655
MA0112.20.848
MA0113.10.456
MA0114.10.598
MA0115.10.0213
MA0116.10.278
MA0117.10.0132
MA0119.10.363
MA0122.10.632
MA0124.10.662
MA0125.10.755
MA0131.10.938
MA0135.10.606
MA0136.15.56362e-11
MA0137.20.27
MA0138.20.405
MA0139.10.265
MA0140.14.62858e-7
MA0141.10.722
MA0142.10.779
MA0143.10.282
MA0144.10.756
MA0145.10.968
MA0146.10.541
MA0147.10.969
MA0148.10.0346
MA0149.10.642
MA0150.10.113
MA0152.10.723
MA0153.10.117
MA0154.10.39
MA0155.10.492
MA0156.14.36057e-9
MA0157.10.0357
MA0159.10.0647
MA0160.10.172
MA0162.10.00726
MA0163.10.0513
MA0164.10.115
MA0258.10.841
MA0259.10.979



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: CNhs11073

Novel motifP-value
10.822
100.0826
1000.0362
1010.623
1020.813
1030.116
1040.87
1050.317
1060.478
1070.226
1080.203
1090.243
110.613
1100.495
1110.968
1120.237
1130.167
1140.165
1150.66
1160.262
1170.0296
1180.512
1190.532
120.765
1200.571
1210.162
1220.379
1230.225
1240.588
1250.614
1260.511
1270.745
1280.362
1290.3
130.318
1300.358
1310.728
1320.136
1330.26
1340.323
1350.628
1360.0649
1370.0697
1380.643
1390.459
140.425
1400.631
1410.615
1420.463
1430.105
1440.46
1450.845
1460.47
1470.142
1480.0379
1490.0836
150.219
1500.459
1510.329
1520.853
1530.328
1540.601
1550.0883
1560.794
1570.99
1580.00329
1590.267
160.683
1600.0193
1610.586
1620.0205
1630.872
1640.748
1650.967
1660.308
1670.739
1680.874
1690.412
170.889
180.988
190.743
20.431
200.466
210.0432
220.456
230.473
240.0982
250.11
260.255
270.426
280.119
290.514
30.453
300.232
310.491
320.0186
330.346
340.325
350.732
360.934
370.146
380.845
390.258
40.847
400.00268
410.586
420.57
430.465
440.849
450.545
460.853
470.934
480.615
490.58
50.799
500.403
510.9
520.856
530.851
540.649
550.915
560.71
570.419
580.0813
590.88
60.806
600.733
610.37
620.11
630.0808
640.479
650.282
660.13
670.804
680.405
690.442
70.514
700.561
710.425
720.187
730.602
740.455
750.0856
760.724
770.0487
780.0363
790.653
80.323
800.465
810.525
820.932
830.367
840.847
850.212
860.224
870.925
880.142
890.373
90.888
900.209
910.508
920.821
930.44
940.536
950.0626
960.341
970.854
980.131
990.00333



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: CNhs11073


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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