Resources

Resources

We collect training and bioinformatic resources in this public Trello board and our code on Github (coppolalab and icnn)


Databases

We are developing a suite of tools for access and mining of gene expression and sequencing data. Apply for an account here, or use the demo (username: demo, password: demo) 

We are collecting mutations and sequence variants responsible for Primary Familial Brain Calcification (or Fahr's disease) here. Contact us if have variants to add. 


REPAIR

REPAIR is a web-based gene expression database for data mining, storage, and in-silico analyses, that allows users to perform custom analysis of datasets by determining their own cut-offs for statistical significance, expression ratios and the like. REPAIR currently has 120 registered users from ~25 Institutions in the US and abroad, and an average traffic of 1,000 searches per month.

There are 2 main ways to query the database: 1) on the main page you can search for one or more genes (separated by comma) across one or more studies; 2) if you click on the "GeneFilter" tab, you can set filters (based on statistical significance, fold change etc) and obtain gene lists. All fold changes are expressed in log2 fold change (so 1 = 2 fold change, -1 = 0.5 fold change).

Short youtube videos:


REPAIR demo1(CHDI gene expression),


REPAIR demo2 (CHDI gene expression)

We worked with the CHDI Foundation to develop HDinHD, a data repository focused on Huntington's disease


GIFTbase

GIFTbase hosts de-identified patient info, genotyping and sequence variation data obtained from our resequencing studies, as well as gene expression data for our dementia and ataxia patient cohorts.


Other Tools

We are developing Winston, an application for grant and personnel financial management. Winston's goal is to provide a general overview of active funds, their current approximate balance, personnel supported by them and (in the future), reminders for timely fund management. 

Use 'demouser' as username and 'demouser' as password to access a fully functioning demo. 

A couple of screencasts describing the main features are at the links below and from within the application. Winston is still being developed and we value your feedback! 


Adding a new Fund


Adding new Personnel


Data

Raw and analyzed data from our published experiments are deposited in the Gene Expression Omnibus repository. Contact us if you have questions! 

Chen JA, Wang Q, Davis-Turak J, Li Y, Karydas AM, Hsu SC, Sears RL, Chatzopoulou D, Huang AY, Wojta KJ, Klein E, Lee J, Beekly DL, Boxer A, Faber KM, Haase CM, Miller J, Poon WW, Rosen A, Rosen H, Sapozhnikova A, Shapira J, Varpetian A, Foroud TM, Levenson RW, Levey AI, Kukull WA, Mendez MF, Ringman J, Chui H, Cotman C, DeCarli C, Miller BL, Geschwind DH, Coppola G. A Multiancestral Genome-Wide Exome Array Study of Alzheimer Disease, Frontotemporal Dementia, and Progressive Supranuclear Palsy. JAMA Neurol. American Medical Association; 2015 Apr 1;72(4):414. PMCID: PMC4397175

Illumina exome arrays, exploring rare coding variation, were run in ~600 subjects and the resulting data deposited into the NIA Genetics of Alzheimer's Disease Data Storage (NIAGADS) repository.


Methods in Molecular Biology

Designing, Performing, and Interpreting a Microarray-Based Gene Expression Study
Giovanni Coppola, MD


Supplementary Material

Annotated Code (advanced draft) [PDF]

Dataset and array annotation files (zip)

Lange et al 2008 (Pubmed)