Workflows

The workflow starts with selecting EH38E2924876 as the search term. Genomic position of provided unique regulatory element identifier was retrieved from CFDE Linked Data Hub[1]. A list of variants in the region of the regulatory element was retrieved from CFDE Linked Data Hub[1]. Variant/variant set associated allele specific epigenomic signatures were retrieved from CFDE LDH[5] based on Roadmap and ENTEx data[6], [4]. GTEx eQTL and sQTL evidence for the given variant(s) were retrieved from CFDE ...

A file containing GEO Aging Signatures was first uploaded. The file containing GEO Aging Signatures was loaded as a gene signature. A file containing GTEx Aging Signatures was first uploaded. The file containing GTEx Aging Signatures was loaded as a gene signature. Significant genes were extracted from the GEO Aging Signatures. Significant genes were extracted from the GTEx Aging Signatures. Reversers and mimickers from over 1 million signatures were identified using SigCom LINCS[1]. Resolved ...

A file was first uploaded. The file was parsed as a gene count matrix. Significantly over-expressed genes when compared to tissue expression in GTEx[1] were identified. RNA-seq-like LINCS L1000 Signatures[3] which mimick or reverse the the expression of IMP3 were visualized. Drugs which down-regulate the expression of IMP3 were identified from the RNA-seq-like LINCS L1000 Chemical Perturbagens[3]. Genes which down-regulate the expression of IMP3 were identified from the RNA-seq-like LINCS L1000 ...

The workflow starts with selecting RPE as the search term. For the given gene ID (SYMBOL), StringDB PPI was extracted using their API[1]. For the Given StringDB PPI, the list of nodes (Gene Set) is generated. For the Given StringDB PPI, the list of nodes (GeneSet) is generated. Reversers and mimickers from over 1 million signatures were identified using SigCom LINCS[2]. The gene set was submitted to Enrichr[4]. The gene set was then searched in the Metabolomics Workbench[5] to identify relevant ...

The workflow starts with a gene set created from Example gene set. CTD is applied which diffuses through all nodes in STRING[1] to identify nodes that are "guilty by association" and highly connected to the initial gene set of interest[2][3]. A list of Highly Connected Genes was obtained from the CTD output. A list of Guilty By Association Genes was obtained from the CTD output.

1. Szklarczyk, D. et al. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic ...

The workflow starts with selecting chr2:g.39417578C>G as the search term. The closest gene to the variant was found using MyVariant.info[1]. Gene expression in tumors for CDKL4 were queried from the Open Pediatric Cancer Atlas API[3]. Median expression of CDKL4 was obtained from the GTEx Portal[4] using the portal's API. To visualize the level of expression across tumor gene expression, a bar plot was created Fig..

1. Lelong, S. et al. BioThings SDK: a toolkit for building high-performance ...

The workflow starts with selecting KLF6 as the search term. RNA-seq-like LINCS L1000 Signatures[1] which mimick or reverse the the expression of KLF6 were visualized. Median expression of KLF6 was obtained from the GTEx Portal[6] using the portal's API. To visualize the scored tissues, a vertical bar plot was created Fig..

1. Evangelista, J. E. et al. SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Research vol. 50 W697–W709 (2022). ...

The workflow starts with selecting chr10:g.3823823G>A as the search term. The closest gene to the variant was found using MyVariant.info[1]. RNA-seq-like LINCS L1000 Signatures[3] which mimick or reverse the the expression of KLF6 were visualized. Median expression of KLF6 was obtained from the GTEx Portal[8] using the portal's API. To visualize the scored tissues, a vertical bar plot was created Fig..

1. Lelong, S. et al. BioThings SDK: a toolkit for building high-performance data APIs in ...

The workflow starts with selecting Autophagy as the search term. Gene sets with set labels containing Autophagy were queried from Enrichr[1]. Identified matching terms from the MGI Mammalian Phenotype Level 4 2019[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for MGI_Mammalian_Phenotype_Level_4_2019. All the identified gene sets were combined using the union set operation. Reversers and mimickers from over 1 million signatures were identified ...

The workflow starts with selecting KLF4 as the search term. Gene sets with set labels containing KLF4 were queried from Enrichr[1]. Identified matching terms from the ENCODE TF ChIP-seq 2015[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ENCODE_TF_ChIP-seq_2015. Identified matching terms from the ChEA 2022[4] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ChEA_2022. Identified ...