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A chip-based assay that allows parallel detection of thousands of samples, such as DNA, at once.

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Why analyse transcriptome instead of proteome?

Analysing the transcriptome (RNA-Seq, microarrays, qPCR etc) is probably the most widely used technology to assess gene expression and dynamic cellular processes. The results are then extrapolated (...
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0answers
15 views

Preprocessing microarray data to detect increased male expression variance due to dosage compensation?

I am currently working with a dataset from a large microarray experiment where one of the aims is to look for evidence of the predicted doubling of variance in expression on the X chromosome in ...
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0answers
12 views

How can the immobilized ssDNA hybrid with another ssDNA in DNA Microarray

In DNA microarray, the template ssDNA (also called oligo or primer) is immobilized on an epoxy-silicane coated glass: The DNA contain primary amine groups on the A, G, and C residues attack the ...
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2answers
29 views

Does PCR amplification affect microarray or DNA biosensor results?

I've noticed that PCR amplification is commonly done before analyzing the DNA sample with microarrays or biosensors. However, won't amplification biases or errors mess up the gene expression profile ...
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1answer
53 views

In microarray normalization, why is the normalization factor this?

I am working on analysis of a huge number of microarray files. I was trying to understand the need for normalization in microarray data and was going through this paper by John Quackenbush(2002). In ...
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0answers
16 views

Microarray with n channels

Recently we've been learning about Microarrays, and the typical method seems to be to run a two channel microarray where your RNA from each cell is labelled with a different fluorescent marker, and ...
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3answers
70 views

How do I score differential activity of cellular pathways in microarray data (not enrichment)?

I would like to identify cellular pathways (KEGG) with discriminative changes in the average activity (expression levels) of their gene members in a two-condition microarray dataset. The goal is to ...
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1answer
87 views

How to determine continental ancestry group (race) with transcriptome data obtained with RNA microarray?

Say I have a whole genome expression data (transcriptome) for some sampled human tissue. Is this data sufficient to find out the continental ancestry group of a donor?
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0answers
29 views

Are the human placenta chorionic villi and villous tree the synonyms?

Are the human placental chorionic villi and the villous tree the synonyms? Or, if not, can I say that these tissues would have practically the same gene expression profile in an RNA microarray ...
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1answer
27 views

What do the intervals between groups of arrays in microarray gene expression data images mean?

This can be a dummy question, but I am not familiar with microarray experiments at all. In this image, what does each of 16 big squares mean, and what are the black intervals between them are? I know ...
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1answer
33 views

Where do I find standard tissue and cell names?

I am developing specialized database on some desease microarray experiments. The initial data is retreived from NCBI and ArrayExpress databases. The problem is that sample attributes sometimes specify ...
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1answer
66 views

Is the technology “identitas v1 forensics chip” related to microarray technology?

Available resource but difficult for me to make scence Relation about crime scene and identitas v1 forensics chip Is the technology "identitas v1 forensics chip" related to microarray technology? ...
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1answer
28 views

Validation by PCR of a lowly expressed gene in microarray

I am interested in validating the precence of a gene (FETUB) whose expression is in the lower quartile of the microarray (see figure in link). https://drive.google.com/open?id=...
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2answers
74 views

How many co-expressed genes would be expected in a tissue?

I am working with gene expression microarrays of tumor tissues and I want to use a program to find the clusters of co-expressed genes in order to know if some particular genes are co-expressed with ...
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2answers
745 views

What is the most appropriate way to normalize gene expression data?

This question comes because reading a paper about normalization of gene-expression data, is not clear if the method for normalize the data is just for RNA-Seq data or could be applied also for ...
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1answer
121 views

How can microarrays be used to quantitatively determine level of gene expression?

This is probably a stupid question because I don't fully understand how microarray experiments work. I'm trying to understand how microarrays work but I'm confused about something which I can't seem ...
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0answers
56 views

What is the aqueous solution for DNA immobilization?

This paper Electric-field assisted immobilization and hybridization of DNA oligomers on thin-film microchips Which is talking about how the electric field improve the DNA immobilization process. ...
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0answers
56 views

Walkthrough Illumina Genotyping

I would love help outlining a basic walkthrough of the wet-lab techniques for processing blood samples from patients, all the way to loading a BeadChip, to the part just before Next Generation ...
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1answer
313 views

What is meant by “the degree to which a gene is expressed” in an individual?

Here is an excerpt from a text that I was reading, Here is an example of microarray data. The idea is to take a group of different individuals and for each of them, you measure how much they do ...
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1answer
166 views

What do HG and NA mean in Geuvadis project RNAseq sample labels?

I'm looking at RNASeq Data from Geuvadis website e.g. the file GD660.GeneQuantRPKM.txt.gz. The samples are labeled by e.g. HG00105.1.M_120209_7 or NA20812.2.M_111216_6 What do HG and NA mean? Are ...
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1answer
99 views

where can I find microarray images?

I have investigated some of the links to known microarray databases, such as arrayTrack, omnibus (NCBI), TCGA. I find that when trying to get microarray images I either get an exotic file format (such ...
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1answer
122 views

Comparison of gene expression time series in vitro and in vivo

I have to analyse two datasets consisting of time-series measurements of gene expression. One set are in vivo data from the expression profiles obtained between a few days before birth to several days ...
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1answer
115 views

Oscillatory electrical system using a chain of neurons

Many daily activities that we perform are result of inbuilt oscillatory circuits in our body. For example walking, breathing, heart beat, blinking, etc. The coding and decoding of stored memory also ...
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1answer
86 views

Genes-of-interest analysis between organisms

I am interested in identifying the differential expression between several genes-of-interest of different organisms. I am trying to assess the benefits of RNA sequencing over microarrays. Both ...
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0answers
166 views

What software/approach to use to build a graph based on microarray gene expression correlation?

What software to use to build a graph based on microarray gene expression mutual correlation? I have tried Cytoscape`s Reactome FI and a recipe from R bioinformatics cookbook, however, need a more ...
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2answers
834 views

How to retrieve full gene names list and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any)?

How to retrieve full gene names and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any other software or language)? Is it possible vice versa: having full gene ...
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1answer
577 views

What to do if microarray t-test, ANOVA, SAM and LImma show various selected significant genes?

Need advice: how to approach discrepancy in differential microarray gene expression test results: what to do if ANOVA, ttest, SAM and Limma procedures show different results and especially more ...
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1answer
29 views

genomatix software linux install [closed]

I have installed the genomatix software which is a jar file the name is InstallChipInspector21.jar.But now I really don;t know how do I start it ,can any one suggest me a method??
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0answers
20 views

How to automate this custom gene expression microarray chip?

I have 16 gene sequences that I am interested in their detection in clinical samples. I already measured their RNA levels by using RT-qPCR technique and their benefit has already been proven to help ...
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1answer
90 views

What makes certain obligate anaerobes viable in fermentation starter cultures?

If Propionibacterium are obligate anaerobes (to wit, poisoned by oxygen), what makes 'Dairy' or classical propionibacteria (e.g. P. shermanii, P. jensenii, P. acidicpropionici, et al) viable in ...
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1answer
319 views

Reusable microarray chips

Microarray chips allow us to conduct many expression experiments in parallel to each other but they can be used only once as far as i know. Are there reusable microarray chips? Have people ever tried ...
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2answers
2k views

Gene perturbation, what is it used for, explain to computer scientists? [closed]

I am trying to build a gene regulation network, and I need some basic knowledge of it. So, in gene research, we perturb genes. Such as knock down them? Can people tell 2 or 3 experiment methods to ...
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1answer
62 views

What information do microarray image convey?

OK I have read that a cell generates 4 kinds of digital (to be precise discrete) data namely DNA, RNA, Protein (sequences that can be encoded as string sequences of nucleotides/ amino acids) and micro ...
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1answer
403 views

Single channel micro arrays

What does single channel microarray mean? When is it used? Thank you for your case in advance.
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0answers
28 views

Are there any differences between qRT-PCR and GEO (microarray data from NCBI) regarding dealing with internal control genes?

As we know, when we do qRT-PCR, the two most commonly used methods are absolute quantification and relative quantification, both the methods are involved in dealing with normalization of house-keeping ...
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1answer
710 views

Microarray gene expression matrix format

After scanning the microarray chip we get RAW data with different formats depending on the type of microarray used. However, these RAW data files can be normalized and processed to generate gene ...
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1answer
270 views

At which step should I apply a detection filter when preprocessing microarray data? (Before/After normalization, batch effects removal)

What is the best practice when preprocessing microarray data using a detection filter (on scanner p-value)? Suppose I have a microarray dataset that I have to normalize with Loess and correct with ...
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1answer
348 views

Microarray data and analysis tools

Microarray has various uses, and to analyse the data a main function classification is used. There are many methods used to classify the data but what are the best and most frequently used methods? ...