Gene Expression Data of Disease vs. Control

Question

[Bioinformatist Newbie]

Hi all,

From several days I am looking for some gene expression dataset on any human disease (heart, brain etc..) where I can find some controlled vs. diseased dataset. I was looking into publications and NCBI GEO but I am unable to find some concrete information. Can anybody guide me in this context?

Thanks.

[Neilfws]

You tagged your question rna-seq, next-gen, so are you interested in datasets using those technologies? GEO is mostly microarray data.

Answer 1

[Evgeniia Golovina]

There are plenty such experiments in GEO db. Open it and search by, for example gene expression, and also you can apply "Expression profiling by high throughput sequencing" filter there.

For example, you can use "Modelling and rescuing neurodevelopmental defect of Down syndrome using induced pluripotent stem cells from monozygotic twins discordant for trisomy 21" experiment [GEO: GSE52249].

Answer 2

[Na Sed]

Please see TCGA database, you can find many data sets.

They are about cancers.

[alolex]

FYI...TCGA contains both microarray and RNA-seq gene expression data that is publicly available. You only need special access if you wanted to access the raw RNA-seq BAM or FASTQ files. Depending on the tumor, many patients have both normal and tumor samples available.

Answer 3

[Giovanni M Dall'Olio]

Clinical expression data is usually restricted for privacy reasons.

You can have a look at the dataset at the European Genome-Phenome archive, but you'll need to submit a project proposal in order to access.

Another source is synapse. For example the AML Prediction challenge provided some expression data, although only for a few proteins.

[Bioinformatist Newbie]

Dear Giovanni,

Can you help me on C: GEO2R Analysis on Cel files downloaded from ArrayExpress ??