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FF:11877-125C5: 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 17:34, 29 March 2012


Name:CD14+ monocytes - treated with Cryptococcus, donor2
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
sexmale
age51
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD4-8
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-Peripheral0.26
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-0.104
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.464
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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-Whole0.189
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: CNhs13487

Jaspar motifP-value
MA0002.24.66306e-7
MA0003.10.286
MA0004.10.358
MA0006.10.872
MA0007.10.778
MA0009.10.286
MA0014.10.922
MA0017.10.0374
MA0018.20.0919
MA0019.10.816
MA0024.10.0017
MA0025.10.0167
MA0027.10.63
MA0028.10.132
MA0029.10.42
MA0030.10.4
MA0031.10.593
MA0035.20.327
MA0038.10.0648
MA0039.20.602
MA0040.10.387
MA0041.10.387
MA0042.10.657
MA0043.13.41601e-4
MA0046.10.0406
MA0047.20.932
MA0048.10.939
MA0050.10.00307
MA0051.10.288
MA0052.10.131
MA0055.10.772
MA0057.10.663
MA0058.10.131
MA0059.10.269
MA0060.13.56396e-11
MA0061.11.35825e-5
MA0062.20.573
MA0065.20.0081
MA0066.10.0373
MA0067.11.04806e-4
MA0068.10.116
MA0069.10.761
MA0070.10.116
MA0071.10.169
MA0072.10.965
MA0073.10.335
MA0074.10.164
MA0076.10.117
MA0077.10.156
MA0078.10.49
MA0079.20.384
MA0080.26.59839e-15
MA0081.12.59886e-4
MA0083.10.846
MA0084.10.341
MA0087.10.796
MA0088.10.548
MA0090.10.179
MA0091.10.474
MA0092.10.265
MA0093.10.355
MA0099.24.37461e-41
MA0100.10.494
MA0101.12.41423e-4
MA0102.23.63202e-6
MA0103.10.57
MA0104.20.678
MA0105.16.16294e-9
MA0106.10.975
MA0107.11.58225e-5
MA0108.20.026
MA0111.10.498
MA0112.22.92458e-5
MA0113.10.944
MA0114.10.166
MA0115.10.844
MA0116.13.14358e-4
MA0117.10.115
MA0119.10.41
MA0122.10.967
MA0124.10.294
MA0125.10.289
MA0131.10.449
MA0135.10.691
MA0136.13.23297e-14
MA0137.20.731
MA0138.20.988
MA0139.10.993
MA0140.10.268
MA0141.10.0493
MA0142.10.324
MA0143.10.458
MA0144.10.229
MA0145.10.284
MA0146.10.112
MA0147.10.726
MA0148.10.782
MA0149.10.209
MA0150.11.41617e-18
MA0152.10.529
MA0153.10.00264
MA0154.10.00129
MA0155.10.647
MA0156.14.08402e-7
MA0157.10.84
MA0159.10.00971
MA0160.10.0206
MA0162.10.983
MA0163.13.30173e-7
MA0164.10.587
MA0258.10.00271
MA0259.10.526



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: CNhs13487

Novel motifP-value
10.106
100.0226
1000.686
1010.843
1020.492
1030.236
1040.574
1050.211
1065.35409e-4
1070.22
1080.928
1090.218
110.156
1100.282
1110.0696
1120.237
1130.552
1140.0206
1150.307
1160.755
1170.0725
1180.184
1190.111
120.342
1200.966
1210.315
1220.557
1230.0743
1240.607
1250.599
1260.222
1270.267
1280.0197
1290.391
130.191
1300.136
1310.569
1320.0612
1330.648
1340.498
1350.435
1360.9
1370.0148
1380.159
1390.0359
140.506
1400.15
1410.307
1420.53
1430.0155
1440.597
1450.511
1460.481
1470.35
1480.0105
1490.589
150.145
1500.48
1510.352
1520.119
1530.443
1540.474
1550.351
1560.756
1570.251
1580.044
1590.703
160.313
1600.352
1610.47
1620.325
1630.229
1640.153
1650.19
1660.447
1670.217
1680.411
1690.0079
170.184
180.0924
190.325
21
200.378
210.379
220.201
230.051
240.308
250.371
260.0603
270.965
280.379
290.367
30.12
300.632
310.718
320.986
330.44
340.428
350.181
360.177
370.0592
380.341
390.731
40.633
400.223
410.0115
420.419
430.0373
440.774
450.61
460.136
470.48
480.447
490.102
50.246
500.988
510.361
520.275
530.331
540.301
550.339
560.66
570.762
580.113
590.0993
60.621
600.0449
610.55
620.0452
630.486
640.434
650.206
660.323
670.536
680.73
690.953
70.261
700.0143
710.0337
720.265
730.117
740.0897
750.106
760.228
770.34
780.0979
790.152
80.336
800.207
810.357
820.0958
830.0582
840.374
850.00807
860.039
870.447
880.569
890.16
90.377
900.0533
910.248
920.173
930.347
940.044
950.373
960.197
970.904
980.113
990.151



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: CNhs13487


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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