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FF:11876-125C4: 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 Salmonella, 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 numberD4-7
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-Peripheral0.743
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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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
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-Whole0.195
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: CNhs13485

Jaspar motifP-value
MA0002.22.32847e-6
MA0003.10.649
MA0004.10.454
MA0006.10.956
MA0007.10.854
MA0009.10.339
MA0014.10.935
MA0017.10.108
MA0018.20.113
MA0019.10.556
MA0024.10.00266
MA0025.10.00553
MA0027.10.616
MA0028.10.0555
MA0029.10.167
MA0030.10.0638
MA0031.10.221
MA0035.20.33
MA0038.10.457
MA0039.20.545
MA0040.10.433
MA0041.10.401
MA0042.10.852
MA0043.18.04194e-8
MA0046.10.0189
MA0047.20.255
MA0048.10.667
MA0050.13.01727e-12
MA0051.12.08086e-7
MA0052.10.265
MA0055.10.614
MA0057.10.453
MA0058.10.224
MA0059.10.267
MA0060.11.19623e-9
MA0061.12.40271e-18
MA0062.20.961
MA0065.20.0277
MA0066.10.102
MA0067.11.67368e-5
MA0068.10.312
MA0069.10.798
MA0070.10.0307
MA0071.10.401
MA0072.10.595
MA0073.10.425
MA0074.10.134
MA0076.10.078
MA0077.10.357
MA0078.10.599
MA0079.20.227
MA0080.27.19344e-12
MA0081.13.7545e-4
MA0083.10.488
MA0084.10.612
MA0087.10.924
MA0088.10.37
MA0090.10.41
MA0091.10.851
MA0092.10.352
MA0093.10.47
MA0099.22.57155e-45
MA0100.10.52
MA0101.11.65064e-21
MA0102.21.16203e-9
MA0103.10.0778
MA0104.20.518
MA0105.12.41957e-20
MA0106.10.816
MA0107.14.76023e-27
MA0108.20.435
MA0111.10.606
MA0112.25.21024e-4
MA0113.10.964
MA0114.10.122
MA0115.10.824
MA0116.13.9741e-4
MA0117.10.0534
MA0119.10.165
MA0122.10.616
MA0124.10.391
MA0125.10.32
MA0131.10.333
MA0135.10.571
MA0136.19.09405e-12
MA0137.20.0637
MA0138.20.322
MA0139.10.689
MA0140.10.402
MA0141.10.138
MA0142.10.415
MA0143.10.89
MA0144.10.0271
MA0145.10.492
MA0146.10.412
MA0147.10.635
MA0148.10.507
MA0149.10.195
MA0150.12.68334e-23
MA0152.10.875
MA0153.10.00192
MA0154.12.84265e-4
MA0155.10.988
MA0156.19.7226e-8
MA0157.10.794
MA0159.10.0384
MA0160.10.067
MA0162.10.884
MA0163.12.10327e-8
MA0164.10.477
MA0258.10.0241
MA0259.10.537



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: CNhs13485

Novel motifP-value
10.112
100.0294
1000.767
1010.903
1020.893
1030.291
1040.572
1050.14
1061.08982e-4
1070.136
1080.754
1090.371
110.175
1100.214
1110.106
1120.428
1130.48
1140.0304
1150.242
1160.962
1170.0704
1180.22
1190.152
120.288
1200.986
1210.774
1220.625
1230.513
1240.577
1250.215
1260.235
1270.573
1280.0475
1290.459
130.139
1300.245
1310.793
1320.109
1330.782
1340.542
1350.724
1360.801
1370.0269
1380.387
1390.129
140.563
1400.31
1410.24
1420.167
1430.026
1440.487
1450.435
1460.631
1470.743
1480.00489
1490.793
150.183
1500.282
1510.574
1520.223
1530.645
1540.615
1550.99
1560.862
1570.443
1580.0309
1590.245
160.366
1600.387
1610.474
1620.172
1630.118
1640.107
1650.17
1660.874
1670.322
1680.119
1690.0253
170.202
180.0895
190.593
20.6
200.205
210.66
220.32
230.0296
240.387
250.532
260.0621
270.567
280.327
290.355
30.131
300.464
310.773
320.543
330.246
340.663
350.13
360.0945
370.067
380.385
390.778
40.943
400.234
410.0165
420.341
430.0182
440.605
450.606
460.174
470.67
480.55
490.132
50.379
500.957
510.535
520.295
530.575
540.446
550.67
560.715
570.82
580.173
590.183
60.805
600.0395
610.653
620.085
630.535
640.538
650.195
660.347
670.501
680.683
690.318
70.299
700.0433
710.0322
720.244
730.179
740.0341
750.184
760.157
770.405
780.128
790.926
80.402
800.218
810.347
820.231
830.0263
840.0432
850.0233
860.0312
870.472
880.741
890.146
90.292
900.0988
910.387
920.247
930.786
940.108
950.652
960.349
970.589
980.173
990.0659



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: CNhs13485


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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