What are the large breast cancer data cohorts besides TCGA?

More Yuanhang Liu's questions See All

Can anyone suggest me some bioinformatics or medical informatics conference that is held in US except ISCB?

03 April 2016 6,490 2 View

Are there any public databases regarding intron retention events in the genome?

10 November 2014 417 4 View

How to fit a heavy-tail distribution?

I have a RNA-seq count data which I suspect to have a Poisson distribution except that the right tail is quit 'heavy'. Does anyone know some heavy-tailed distribution? It would be better if it...

09 October 2013 7,239 6 View

Transcription factor enrichment tools?

I have a set of genes and I want to know which transcription factors are overrepresented in these genes. I know tools like MEME, but I have to provide the sequence rather than just gene names to...

09 October 2013 3,300 11 View

Maximum likelihood estimation for a bi-model data?

I have an expression data. My hypothesis is that it is a combination of two models, negative binomial(NB) and Poisson. Currently, I'd like to do a simulation. Firstly I want to estimate the...

08 September 2013 4,201 2 View

Could anyone recommend some literature about network modeling?

I want to do a project on network modeling, interest especially lies in gene-gene network and miRNA-mRNA network. Could anyone recommend some literature to start with?

07 August 2013 1,165 3 View

What are the causes of reads mapped to intergenic region in RNA-seq?

After we align our data onto genome using Tophat. I always see reads mapped to the intergenic region. It only accounts for a very small portion though. Could anyone enlighten me on this? What are...

06 July 2013 1,844 20 View

How to determine whether a gene is expressed in RNA-seq?

What statistic test I can use to prove that a gene is expressed in RNA-seq? For example, after RNA-seq, one gene has a RPM of 100, how can I determine this gene is expressed? Another way to think...

05 June 2013 1,617 10 View

Could anyone recommend to me one bioinformatics algorithms book or other related resource?

I am kind of stuck when trying to find new algorithms.

05 June 2013 7,233 4 View

Anyone use Kmeans clustering method on microarray gene expression data?

What difference would it have to do a standardized step before kmeans analysis?

03 April 2013 3,947 12 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Does Napabucasin soluble in dichloromethane and in ethanol?

I need to prepare a solution of Napabucasin (inhibitor of cancer cell stemness) in dichloromethane. The drug is expensive, so maybe somebody already tried to do it. If it is soluble, what is the...

02 March 2021 9,945 3 View

New Journal, "Integrative Psychological and Behavioral Science" -- do you not know, and have you not seen, this done before?

Question to you and THEM, the New Journal, "Integrative Psychological and Behavioral Science" -- do you not know, and have you not seen, this done before? There appears to be a core problem for...

02 March 2021 3,024 2 View

Could you please recommend some good journal that accept very long revie papers (approximately 6000+ words) in neurosurgery, cancer biology ?

01 March 2021 8,087 3 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Is CD44 degraded in lysosome together with hyaluronan after CD44 mediated endocytosis of hyaluronic acid?

Also when RHAMM binds hyaluronic acid, they get internalized, will RHAMM also be degraded? Or both CD44 and RHAMM will be transferred back to the cell membrane? Asking for breast cancer cell line...

01 March 2021 8,169 2 View

Where to find data on trees in tropical agroforestry?

Hi, I'm looking for data (mainly related to management: growth rate, canopy size, soil and climate preferences, etc.) about tropical trees used in tropical agroforestry. Have you ever heard about...

28 February 2021 7,356 8 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Antonio Colaprico

Hi Yuanhang Liu,

for breast cancer subtypes I suggest you to try this functions:

dataSubt table(dataSubt$PAM50)

Basal Her2 LumA LumB Normal

98 58 232 129 30

and then you can search in GEO like breast and subtype you need (eg. GSE65212 ...)

For the moment I can suggest you start looking at our recent package TCGAbiolinks. I will appreciate if you could help me by means of feedbacks or comments.

For further informations or collaborations you can write me ([email protected]).

Consider if we are able we can add features or functionalities you need into the package.

Best,

Article TCGAbiolinks: An R/Bioconductor package for integrative anal...