Tools

A) Cancer tools

Web resources to compare results obtained in integrative approaches of different types of cancer, with the groups of proteins, genes and biological pathways of your research:

1. MetaFun-NSCLC:  Functional signatures in non-small-cell lung cancer. Webtool. Publication
2. MetaFun-PDAC: A comprehensive transcriptional signature in pancreatic ductal adenocarcinoma reveals new insights into the immune and desmoplastic microenvironments.  Webtool. Publication
3. MetaFun-ExoCellBC: Comparative profiling of whole-cell and exosome samples reveals protein signatures that stratify breast cancer subtypes. Webtool. Publication
4. MetaFun-MBM: Unveiling common transcriptomic features between melanoma brain metastases and neurodegenerative diseases. Webtool. Preprint
5. MetaFun-BC: DNA methylation signatures in breast cancer. Webtool. Preprint

B) Neuroscience resources

Web tools to identify transcriptomic and lipidomic signatures to improve diagnosis and treatment of brain diseases:

1. Transcriptomic signatures in neurodegenerative diseases:
   1. MetaFun-PD: Unveiling sex-based differences in Parkinson Disease: a comprehensive meta-analysis of transcriptomic studies. Webtool. Publication.
   2. MetaFun-MS: A deep transcriptome meta-analysis reveals sex differences in Multiple Sclerosis. Webtool. Publication. 
   3. MetaFun-AD: An integrated approach to identify sex-specific genes, transcription factors, and pathways in Alzheimer’s disease. Webtool. Publication
   4. MetaFun-AD-miRNA: The role of microRNAs to understand sex-based differences in Alzheimer’s disease. Webtool. Publication.
2. sc-RNA-seq atlas in neurodegenerative diseases:
   1. CBL-atlas-Multiple Sclerosis: Single cell landscape of sex differences in the progression of multiple sclerosis. Webtool. Preprint.
   2. CBL-atlas-Parkinson Disease: Single cell RNA seq metaanalysis reveals a higher neurodegenerative and inflammatory profile in males in Parkinson’s Disease (in progress). Webtool
   3. CBL-atlas-Alzheimer Disease: Webtool
3. MetaFun-SCI: A spinal cord injury time and severity consensus transcriptomic reference suite in rat reveals translationally-relevant biomarker genes. Webtool. Preprint 
4. MetaFun-SCZ: The impact of sex on gene expression in the brain of schizophrenic patients. Webtool. Publication
5. Study of differential sex profiles in neuroinflammation associated with alcohol use disorders:
   1. MetaFun-AUD: Unveiling sex-based differences in the effects of alcohol abuse. Webtool. Publication 
   2. MetaFun-SAL-chronics: Novel insight into the lipid network of plasma extracellular vesicles reveal sex-based differences in the lipidomic profile of alcohol use disorder patients.  Webtool. Publication
   3. MetaFun-SAL: Lipidomic landscape of circulating extracellular vesicles isolated from adolescents exposed to ethanol intoxication: a sex difference study. Webtool. Publication.

C) Metabolic diseases tools

Open tools for the analysis of metabolic disease omics data:

1. MetaFun-NAFLD: Hepatic steatosis and steatohepatitis: a functional meta-analysis of sex-based differences in transcriptomic studies. Webtool. Publication
2. MetaFun-HFD: Integrated transcriptomic landscape of the effects of anti-steatotic treatments in mouse models of fatty liver disease. Webtool. Publication
3. MetaFun-HKG: Deciphering the sex bias in housekeeping gene expression in adipose tissue.  Webtool. Publication

D) Sex differences tools

Tools to identify and understand the molecular mechanisms underlying sex differences in biomedical studies:

1. Brain diseases:  
   • a) Gene/miRNA signatures in neurodegenerative diseases: a1) Parkinson Disease; a2) multiple sclerosis; a3) Alzheimer Disease – genes; a4) Alzheimer Disease – miRNAs
   • b) sc-RNA-seq atlas in neurodegenerative diseases: b1) multiple sclerosis; b2) Parkinson Disease; b3) Alzheimer Disease
   • c) Alcohol use disorders: c1) Gene expression signatures; c2) plasma extracellular vesicles; c3) circulating extracellular vesicles in adolescents
   • d) Schizophrenia
2. Metabolic disorders:  a) NAFLD; b)  HKG
3. Cancer:  non-small-cell lung cancer 
4. MetaFun: unveiling sex-based differences in multiple transcriptomic studies through comprehensive functional meta-analysis

MetaFun

Unveiling Sex-based Differences in Multiple Transcriptomic Studies through Comprehensive Functional Meta-analysis

While sex-based differences in various health scenarios have been thoroughly acknowledged in the literature, we lack a deep analysis of sex as a variable in this context. To fill this knowledge gap, we created MetaFun as an easy-to-use web-based tool to meta-analyze multiple transcriptomic datasets with a sex-based perspective to gain major statistical power and biological soundness. Furthermore, MetaFun can be used to perform case-control meta-analyses, allowing researchers with basic programming skills to access this methodology. Publication