How can I extract cluster information from a correlation gene expression matrix?

More Francisco J. Enguita's questions See All

Do you have a template for miRNA qPCR arrays from Qiagen (former Exiqon)?

Dear colleagues After a lot of struggle with the new rebranding of Exiqon that sold the LNA technology to Qiagen, we decided to give a try to the new miRNA qPCR arrays. We bought the whole...

11 December 2019 7,166 3 View

How to refine a protein-drug complex structure coordinates?

I have a protein-drug complex obtained by virtual drug screening. How can I refine the coordinates of the whole complex?. Is energy minimization the best protocol to be applied? Thanks in...

03 April 2019 8,863 3 View

RNAse R... which supplier?

Dear All I am looking forward to treat my total RNA samples with RNAse R. Any suggestions about which supplier do you prefer for purchasing it?. Thanks. Best

09 October 2018 9,518 5 View

How to over-express a selected circular RNA?

Dear All Do you have experience in methods for the over-expression of selected circular RNAs in human or mouse cells?... If yes... which strategy did you use?... which vectors and...

06 July 2018 7,681 1 View

What is your favourite Gene-enrichment analysis in a graphical environment?

Hi there I would like to know and to get your feedback about you favourite Gene-enrichment analysis software based in a graphical environment, preferably on-line. Please give me your feedback...

05 June 2018 9,060 9 View

How is the performance of Nanostring system to detect extracellular miRNAs?

Dear All I wanted to give a try to Nanostring system to detect extracellular miRNAs in a screening-based approach. I am wondering if some of you have experience with Nanostring in the detection...

05 June 2018 7,635 3 View

Someone has experience with the new Exiqon-Qiagen miRNAnome qPCR screening panels?

Dear All I had used for a while the Exiqon miRNAnome panels based on low density qPCR arrays. However, since the begginning of this 2018, Exiqon has joined Qiagen. I ordered the same screenings...

01 February 2018 2,140 16 View

How to compare two XPM contact matrices generated by GROMACS?

Hi there I got several contact matrices in XPM format generated by GROMACS trajectories for a series of protein mutants. How to compare them to extract the differences between atom contacts in...

11 December 2017 8,959 12 View

Any web-based tool to get statistics about location and miRNA expression?

Hi there I am dealing with a long list of miRNAs... I would like to get some tool to organize them by functional groups, clusters, chromosome location, tissue expression, etc... Any suggestion?....

09 October 2017 8,554 4 View

Is there any alternative to Green A Dyematrex gel (Amicon) for pseudo-affinity chromatography?

I am trying to reproduce an old purification protocol from 2004 that claims the use of a pseudo-affinity chromatography based on Green A Dyematrex gel (Amicon). The product is discontinued from...

08 September 2016 1,990 3 View

Weak DAPI staining after immunohistochemistry - how to improve?

After immunohistochemistry of previously fixed in PFA and EtOH and then frozen 20 μm sections of zebrafish brain, DAPI staining is very weak (right) compared to the same sections stained without...

05 August 2024 9,637 2 View

If we are using snowball sampling technique, how do we justify the true representativeness of the sample statistically? is there any statistical test?

Are there any statistical methods to justify your sampling technique using SPSS or AMOS?

05 August 2024 9,153 4 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

Why my colony PCR results of my recombinant bacterial not showing any results?

I am performing ligation of the plasmid and a target gene. The steps I have taken are: 1. Double digestion of the plasmid and target gene 2. Ligation of the plasmid with the target gene 3....

05 August 2024 2,570 3 View

The Curse of Evolution and Complexity?

Brain and body mass together are positively correlated with lifespan (Hofman 1993). The duration of neural development is one of the best predictors of brain size, and conception is the best...

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What are possible strategies can be used to analyze data under sequential explanatory mixed method approach?

Better ways to analyze the qualitative and quantitative data in a sequential explanatory mixed method approaches

04 August 2024 2,703 6 View

Why 3 replicates for most biological assays? Is it enough to examine the data fits normal distribution?

Just bounced on me. Before statistically analysing significant difference, shouldn't we see if data fits normal distribution first? Is 3 replicates enough to testify the hypothesis of normal...

31 July 2024 8,141 13 View

What is the acceptable p-value cutoff for GO enrichment analysis ?

I have an RNA-seq data that I have analysed using Limma-voom and have extracted the gene IDs, log2FC and the p-values. At p value < 0.05, I have over 10,000 DEGs, however, when I run the GO...

31 July 2024 225 2 View

Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

30 July 2024 6,420 1 View

Seeking Software Recommendations for SELEX NGS Data Analysis?

I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed

30 July 2024 1,061 5 View

Dave Lee

Hi Francisco,

Have you considered using R? There are a couple of quick and easy functions that you can use that might help you with your problem.

Hierarchial clustering could be a good first port of call to visualise your expression data.

Matej Lexa

Hi,

CLUTO program by G.Karypis contains an "scluster" function that does hierarchical clustering on such data.

Francisco J. Enguita

THanks Dave and Matej. Unfortunately, I have not so much time to learn R... I will try CLUTO...

Anupam Singh

You can also try Cluster 3.0. It has both hierarchical clustering as well as k-mean clustering.

http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm