The CommonMind Consortium

Objective

• find an annotation source: anything from a database, a publication or a website
• ideally something downloadable that can be used to annotate my dataset
• basically, anything that will give extra information about my dataset that will help in further analyses

Duration

Expected: 1 hr

Actual: 2 hr

Procedure

• read through my study again: Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis
• thought about what data might be useful
• found that the study mentions the CommonMind Consortium
• the paper states that: "IGF2 was found to be the top downregulated gene in the schizophrenia prefrontal cortex in the large CommonMind consortium RNA-sequencing study"

Results

What sort of data is it? What sort of information does it offer us?

Large-scale genetics studies have identified genomic regions associated with disease risk, but less is known about the molecular mechanisms by which risk alleles with small effects lead to schizophrenia and bipolar disorder. The CommonMind Consortium aims to fill the gap between genetics and disease phenotype. The consortium provides functional genomic data from the dorsolateral prefrontal cortex specimens. It has compiled a functional genomics resource in order to understand the interplay between genetic regulation, gene expression, chromatin accessibility, and disease in the human brain (Hoffman et al., 2019).

When and where was it published? Was it published?

The first release was in March 2015. The associated paper was published in September 2019. It was published on the Synapse platform. (Release Notes, n.d.)

Is this annotation set updated regularly or is it a static source?

The website has releases about twice per year.

Where can I find this data? (link to the download web address or ftp site or publication where it can be found)

The data can be found on the CommonMind Consortium Knowledge Portal, more specifically can be found in the tables in the portal. The data can also be downloaded programmatically through packages in R (synapser package) or Python (synapseclient package) (Downloading data programmatically, n.d.).

How is the data formatted and released? Does it exist in some sort of standard file format?

The data can be downloaded in CSV format (Downloading data from the synapse UI, n.d.). The resource also provides raw FASTQ and BAM files (Hoffman et al., 2019).

What identifiers are associated with these annotations?

The CommonMind Consortium is available on the Synapse platform which uses its own identifier called SynID.

Conclusion and Outlook

Note: this data is only available with an account

References

Hoffman, G.E., Bendl, J., Voloudakis, G. et al. CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder. Sci Data 6, 180 (2019). https://doi.org/10.1038/s41597-019-0183-6

Release Notes. Synapse. (n.d.). Retrieved March 6, 2023, from https://www.synapse.org/#!Synapse:syn2759792/wiki/194733

Downloading data programmatically. Welcome. (n.d.). Retrieved March 6, 2023, from https://help.synapse.org/docs/Downloading-Data-Programmatically.2003796248.html

Downloading data from the synapse UI. Welcome. (n.d.). Retrieved March 6, 2023, from https://help.synapse.org/docs/Downloading-Data-From-the-Synapse-UI.2004254837.html