Thoughts on transcription

A few weeks ago I asked this question: Transcription requires RNA pol; RNA pol requires the transcription of RNA pol subunits. Where did the first RNA pol come from? Silly Q? — Dave Tang (@davetang31) January 29, 2015

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Genomic Regions Enrichment of Annotations Tool

The Genomic Regions Enrichment of Annotations Tool (GREAT) is a tool that allows you to find enriched ontological terms in a set of genomic regions. This talk (running time ~1 hour) gives an overview of the tool. In brief, GREAT is an alternative to gene-centric enrichment tools such as DAVID and uses a binomial test…

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Rett syndrome and piRNAs

Two years ago we were invited to write an article in a Special Issue of the Disease Markers journal, which was dedicated to autism spectrum disorders (ASD) and biomarkers. From Wikipedia, ASD are disorders characterised by social deficits and communication difficulties, stereotyped or repetitive behaviours and interests, and in some cases, cognitive delays.

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Analysing miRNA expression in cancers

MiRNAs are a class of small RNAs that when expressed usually down regulates the expression of its target transcript by binding to it and causing it to degrade or inhibiting it from being translated. There has been a lot of interest in studying the expression pattern of miRNAs, especially in relation to cancer, since their…

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Tissue specificity

Updated 2017 October 14th A key measure in information theory is entropy, which is the amount of uncertainty involved in a random process; the lower the uncertainty, the lower the entropy. For example, there is lower entropy in a fair coin flip versus a fair die roll since there are more possible outcomes with a…

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How deep should we sequence?

Updated 2013 November 12th. High throughput sequencers are continually increasing their output of reads; according to Illumina, the HiSeq2500/1500 can output a maximum of 187 million single end reads per lane/flow cell. The question is “How deep should we sequence our samples?” Obviously it depends on the aim; if we wish to profile lowly expressed…

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Fitting a Michaelis-Menten curve using R

Updated 2017 November 22nd Many biological phenomena follow four different types of relationships that include sigmoid, exponential, linear and Michaelis-Menten (MM) type relationships. The MM model is given by where is the reaction rate of product to substrate , represents the maximum rate achieved by the system, and is the substrate concentration at which the…

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Epigenetics

For the past week I’ve been attending the: Karolinska Institutet – RIKEN Joint International Doctoral Course on “Epigenomics: Methods and Applications to Disease and Development” Today is the last day of the course and the course participants have to come up with a proposal that combines epigenetics and its application to a particular disease (our…

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Motifs upstream of RefSeq gene models

Here’s a very primitive way of looking for motifs upstream of RefSeq gene models. 1) Download the upstream sequences (-50) of RefSeq gene models using the UCSC Table Browser tool as a bed file 2) Using the fastaFromBed tool from BEDTools, make fasta files from the bed file 3) Look for motifs Here’s the main…

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Why miRNA are 22 or 23 nucleotides long

Late last year I mapped random sized DNA sequences back to the genome. The purpose was simply to see how long sequenced reads needed to be before they could be uniquely mapped to the genome. I couldn’t find the statistics on this, so I just did it myself. I didn’t dwell on the results too…

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