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FF:11867-125B4: 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 17:33, 29 March 2012


Name:CD14+ monocytes - treated with Cryptococcus, donor1
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
sexfemale
age69
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD3-8
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-Peripheral0.288
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-0.00693
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.589
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.493
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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-Whole0.244
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: CNhs13472

Jaspar motifP-value
MA0002.21.1074e-7
MA0003.10.307
MA0004.10.446
MA0006.10.797
MA0007.10.757
MA0009.10.196
MA0014.10.938
MA0017.10.0495
MA0018.20.188
MA0019.10.539
MA0024.10.00146
MA0025.10.0196
MA0027.10.965
MA0028.10.171
MA0029.10.283
MA0030.10.447
MA0031.10.611
MA0035.20.216
MA0038.10.0337
MA0039.20.709
MA0040.10.244
MA0041.10.165
MA0042.10.542
MA0043.13.05495e-4
MA0046.10.0319
MA0047.20.915
MA0048.10.882
MA0050.15.12377e-4
MA0051.10.167
MA0052.10.319
MA0055.10.74
MA0057.10.65
MA0058.10.248
MA0059.10.348
MA0060.15.11451e-12
MA0061.14.59547e-5
MA0062.20.581
MA0065.20.00931
MA0066.10.0202
MA0067.16.86152e-4
MA0068.10.184
MA0069.10.839
MA0070.10.0434
MA0071.10.224
MA0072.10.834
MA0073.10.333
MA0074.10.122
MA0076.10.132
MA0077.10.155
MA0078.10.481
MA0079.20.415
MA0080.23.95088e-15
MA0081.12.75899e-4
MA0083.10.836
MA0084.10.721
MA0087.10.857
MA0088.10.521
MA0090.10.197
MA0091.10.544
MA0092.10.224
MA0093.10.483
MA0099.23.33048e-40
MA0100.10.589
MA0101.14.72259e-4
MA0102.23.14091e-7
MA0103.10.542
MA0104.20.896
MA0105.12.53292e-8
MA0106.10.808
MA0107.14.38552e-5
MA0108.20.00813
MA0111.10.458
MA0112.25.22809e-5
MA0113.10.77
MA0114.10.201
MA0115.10.763
MA0116.12.92398e-4
MA0117.10.18
MA0119.10.317
MA0122.10.857
MA0124.10.938
MA0125.10.284
MA0131.10.408
MA0135.10.718
MA0136.16.24254e-15
MA0137.20.721
MA0138.20.859
MA0139.10.996
MA0140.10.118
MA0141.10.0466
MA0142.10.798
MA0143.10.652
MA0144.10.311
MA0145.10.241
MA0146.10.0803
MA0147.10.924
MA0148.10.828
MA0149.10.199
MA0150.11.46344e-15
MA0152.10.518
MA0153.10.0011
MA0154.10.00204
MA0155.10.58
MA0156.12.44518e-7
MA0157.10.967
MA0159.10.0109
MA0160.10.0246
MA0162.10.667
MA0163.12.91309e-7
MA0164.10.561
MA0258.10.00263
MA0259.10.562



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: CNhs13472

Novel motifP-value
10.0921
100.0236
1000.816
1010.87
1020.523
1030.275
1040.564
1050.254
1065.59661e-4
1070.164
1080.868
1090.201
110.115
1100.256
1110.0201
1120.242
1130.586
1140.011
1150.427
1160.717
1170.0461
1180.174
1190.142
120.352
1200.985
1210.496
1220.736
1230.0857
1240.53
1250.395
1260.218
1270.295
1280.0164
1290.524
130.18
1300.124
1310.656
1320.108
1330.699
1340.536
1350.331
1360.836
1370.00948
1380.192
1390.018
140.467
1400.0946
1410.341
1420.462
1430.0171
1440.684
1450.4
1460.439
1470.423
1480.00773
1490.581
150.135
1500.474
1510.306
1520.139
1530.509
1540.58
1550.326
1560.792
1570.285
1580.0556
1590.918
160.303
1600.356
1610.474
1620.531
1630.188
1640.0862
1650.162
1660.52
1670.214
1680.34
1690.0073
170.165
180.11
190.272
20.974
200.336
210.349
220.219
230.0406
240.369
250.41
260.0328
270.974
280.494
290.274
30.0895
300.529
310.743
320.875
330.407
340.471
350.132
360.148
370.0717
380.331
390.682
40.851
400.184
410.0124
420.375
430.0332
440.757
450.698
460.118
470.456
480.398
490.0917
50.234
500.992
510.333
520.29
530.361
540.295
550.482
560.647
570.751
580.135
590.107
60.514
600.0379
610.49
620.049
630.434
640.396
650.184
660.193
670.444
680.639
690.888
70.266
700.0114
710.0318
720.251
730.13
740.101
750.0846
760.26
770.359
780.0685
790.0537
80.287
800.27
810.367
820.0732
830.26
840.423
850.00693
860.0626
870.496
880.614
890.175
90.319
900.0651
910.283
920.172
930.413
940.0301
950.31
960.377
970.914
980.127
990.168



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: CNhs13472


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)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000860 (classical monocyte)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002057 (CD14-positive, CD16-negative classical monocyte)
0002087 (nongranular leukocyte)
0002194 (monopoietic 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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