Journal: Nucleic Acids Research

Article Title: HumanNet v3: an improved database of human gene networks for disease research

doi: 10.1093/nar/gkab1048

Figure Lengend Snippet: Comparison between HumanNet v2 and v3

Article Snippet: DP , Based on domain profiles by InterPro r46 Profile , Based on domain profiles by InterPro r84 Profile.

Techniques: Microarray, shRNA, CRISPR, Functional Assay

Journal: Nature Genetics

Article Title: Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction

doi: 10.1038/ng.3010

Figure Lengend Snippet: ( a ) Normalized transcript levels of the 44 genes encoding WAP domain–containing proteins in T. muris , comparing the parasite anterior region with the posterior regions of adult female (F) and male (M) parasites. Indication of significant transcriptional upregulation in a particular pairwise comparison (Up) refers to false discovery rate (FDR) % 0.01 and FDR % 1 × 10 −5 when denoted by one asterisk and to FDR % 1 × 10 −5 when denoted by two asterisks. SP, signal peptide; WAP, whey acidic protein (Interpro, IPR008197 ); WR1, cysteine-rich repeat ( IPR006150 ); TIL, trypsin inhibitor–like ( IPR002919 ). For a full version of this figure, see . ( b ) Sequence logos show the conserved and distinct sequence characteristics of the WAP domains (Interpro, IPR008197 ) found in proteins from H. sapiens , T. trichiura and T. muris . The four canonical disulfide bonds formed by eight cysteine residues are highlighted at the top of the sequence logo for human WAP domains. The sequence logos representing the different species are aligned around the central CXXDXXC motif (where X is any amino acid). For a full version of this figure, see .

Article Snippet: Functional gene annotation including the assignment of gene product descriptions and GO terms was based on Interpro protein domain analysis and BLAST searches against annotated genomes.

Techniques: Comparison, Sequencing

Journal: Journal of Structural and Functional Genomics

Article Title: The Protein Model Portal

doi: 10.1007/s10969-008-9048-5

Figure Lengend Snippet: Typical view of a model detail page. Information about the model provider, the segment of the target protein (e.g., MLP-like protein 34; Arabidopsis thaliana) covered by the model, and the template structure used for model building, are stored in the portal database. All other information required for building the webpage, such as the coordinates of the model, the PFAM domain structure, and UniProt annotation of the protein sequence, is retrieved dynamically

Article Snippet: The domain structure of the target sequence is displayed based on PFAM domain annotation [ ] which is retrieved dynamically from the InterPro database.

Techniques: Sequencing