Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700™/Panther™ probe-to-gene annotations

Noth, Sebastian; Benecke, Arndt

doi:10.1186/1471-2105-6-307

Cited by 29 publications

(15 citation statements)

References 8 publications

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“…Data quality was determined using a QC procedure [40] . Data were normalized using NeONORM with k = 0.02 [41–43] . Subtraction profiling was performed as described previously [44,45] using the CDS test [46] .…”

Section: Methodsmentioning

confidence: 99%

A TDG/CBP/RARα Ternary Complex Mediates the Retinoic Acid-Dependent Expression of DNA Methylation-Sensitive Genes

Léger

Smet‐Nocca

Attmane-Elakeb

et al. 2014

Genomics, Proteomics &Amp; Bioinformatics

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The thymine DNA glycosylase (TDG) is a multifunctional enzyme, which is essential for embryonic development. It mediates the base excision repair (BER) of G:T and G:U DNA mismatches arising from the deamination of 5-methyl cytosine (5-MeC) and cytosine, respectively. Recent studies have pointed at a role of TDG during the active demethylation of 5-MeC within CpG islands. TDG interacts with the histone acetylase CREB-binding protein (CBP) to activate CBP-dependent transcription. In addition, TDG also interacts with the retinoic acid receptor α (RARα), resulting in the activation of RARα target genes. Here we provide evidence for the existence of a functional ternary complex containing TDG, CBP and activated RARα. Using global transcriptome profiling, we uncover a coupling of de novo methylation-sensitive and RA-dependent transcription, which coincides with a significant subset of CBP target genes. The introduction of a point mutation in TDG, which neither affects overall protein structure nor BER activity, leads to a significant loss in ternary complex stability, resulting in the deregulation of RA targets involved in cellular networks associated with DNA replication, recombination and repair. We thus demonstrate for the first time a direct coupling of TDG’s epigenomic and transcription regulatory function through ternary complexes with CBP and RARα.

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Section: Methodsmentioning

confidence: 99%

A TDG/CBP/RARα Ternary Complex Mediates the Retinoic Acid-Dependent Expression of DNA Methylation-Sensitive Genes

Léger

Smet‐Nocca

Attmane-Elakeb

et al. 2014

Genomics, Proteomics &Amp; Bioinformatics

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“…Note that we renormalized the resulting data according to the median once more after having removed probes for which the software has set flags equal to or greater than 2 12 , indicating compromised or failed measurements (as recommended by Applied Biosystems). This secondary normalization is implemented in the ace.map suite that we developed ( 39 ).…”

Section: Methodsmentioning

confidence: 99%

High-Sensitivity Transcriptome Data Structure and Implications for Analysis and Biologic Interpretation

Noth

Brysbaert

Pellay

et al. 2006

Genomics, Proteomics &Amp; Bioinformatics

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Novel microarray technologies such as the AB1700 platform from Applied Biosystems promise significant increases in the signal dynamic range and a higher sensitivity for weakly expressed transcripts. We have compared a representative set of AB1700 data with a similarly representative Affymetrix HG-U133A dataset. The AB1700 design extends the signal dynamic detection range at the lower bound by one order of magnitude. The lognormal signal distribution profiles of these high-sensitivity data need to be represented by two independent distributions. The additional second distribution covers those transcripts that would have gone undetected using the Affymetrix technology. The signal-dependent variance distribution in the AB1700 data is a non-trivial function of signal intensity, describable using a composite function. The drastically different structure of these high-sensitivity transcriptome profiles requires adaptation or even redevelopment of the standard microarray analysis methods. Based on the statistical properties, we have derived a signal variance distribution model for AB1700 data that is necessary for such development. Interestingly, the dual lognormal distribution observed in the AB1700 data reflects two fundamentally different biologic mechanisms of transcription initiation.

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“…For microarray analyses, hybridization and detection were performed following the protocols supplied by Illumina using the HumanHT-12 v4 Expression BeadChip Kit and an iScan system (both Illumina). The raw data were quality controlled 57 , NeoNORM normalized using k = 0.2 58 , and analyzed as outlined in 59 . For subtraction profiling we used the CDS statistical test 60 with a positive False Discovery Rate correction where appropriate.…”

Section: Methodsmentioning

confidence: 99%

HIC1 controls cellular- and HIV-1- gene transcription via interactions with CTIP2 and HMGA1

Douce

Forouzanfar

Eilebrecht

et al. 2016

Sci Rep

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Among many cellular transcriptional regulators, Bcl11b/CTIP2 and HGMA1 have been described to control the establishment and the persistence of HIV-1 latency in microglial cells, the main viral reservoir in the brain. In this present work, we identify and characterize a transcription factor i.e. HIC1, which physically interacts with both Bcl11b/CTIP2 and HMGA1 to co-regulate specific subsets of cellular genes and the viral HIV-1 gene. Our results suggest that HIC1 represses Tat dependent HIV-1 transcription. Interestingly, this repression of Tat function is linked to HIC1 K314 acetylation status and to SIRT1 deacetylase activity. Finally, we show that HIC1 interacts and cooperates with HGMA1 to regulate Tat dependent HIV-1 transcription. Our results also suggest that HIC1 repression of Tat function happens in a TAR dependent manner and that this TAR element may serve as HIC1 reservoir at the viral promoter to facilitate HIC1/TAT interaction.

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Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700™/Panther™ probe-to-gene annotations

Cited by 29 publications

References 8 publications

A TDG/CBP/RARα Ternary Complex Mediates the Retinoic Acid-Dependent Expression of DNA Methylation-Sensitive Genes

A TDG/CBP/RARα Ternary Complex Mediates the Retinoic Acid-Dependent Expression of DNA Methylation-Sensitive Genes

High-Sensitivity Transcriptome Data Structure and Implications for Analysis and Biologic Interpretation

HIC1 controls cellular- and HIV-1- gene transcription via interactions with CTIP2 and HMGA1

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