Journal: eLife

Article Title: Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks

doi: 10.7554/eLife.02725

Figure Lengend Snippet: Pathways most significantly affected by exonic indels DOI: http://dx.doi.org/10.7554/eLife.02725.031 10.7554/eLife.02725.032 Table 2—source data 1. Results of pathway enrichments, custom definition of the DSBR by HR pathway and the allelic frequencies of mutations in HR genes. DOI: http://dx.doi.org/10.7554/eLife.02725.032

Article Snippet: BioCarta (ranking by GenomeMusic) , ATR/BRCA pathway , 1 , 1.0E−16 , 15 , 3.50.

Techniques: Homologous Recombination, Non-Homologous End Joining, Activation Assay

Journal: BMC Plant Biology

Article Title: Dynamic transcriptome analysis identifies genes related to fatty acid biosynthesis in the seeds of Prunus pedunculata Pall

doi: 10.1186/s12870-021-02921-x

Figure Lengend Snippet: Proposed fatty acid biosynthesis pathway for P. pedunculata seeds. a General view of the fatty acid biosynthesis pathway based on the KEGG pathway annotation. The blocks in red represent the genes differentially expressed during the seed development of P. pedunculata . b Working model for the genes involved in the fatty acid and TAG biosynthesis in P. pedunculata . Heat maps represent the expression levels (scaled values) of genes in the developing seeds of P. pedunculata . DAG: 1,2-Diacylglycerol; PA: phosphatidic acid; LPA: lysophosphatidic acid; G-3-P: glycerol-3-phosphate; PC: phosphatidylcholine; LPC: lysophosphatidylcholine, and glycerol; MAG: monoacylglycerol; PDH: pyruvate dehydrogenase complex; ACCA: acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha; ACP: acyl carrier protein; MAT: malonyl-CoA-acyl carrier protein transacylase; KAS: ketoacyl-ACP synthase; EAR: enoyl-ACP reductase; KAR: ketoacyl-ACP reductase; HAD: hydroxyacyl-ACP dehydrase; FAD: fatty acid desaturase; SAD: 18:0-ACP desaturase; FATB: acyl-ACP thioesterase B; FATA: acyl-ACP thioesterase A; DGAT: diacylglycerol acyltransferase; PAH: phosphatidic acid phosphohydrolase; LPAT: acyl-CoA:acylglycerol-3-phosphate acyltransferase; GPAT: glycerol-3-phosphate acyltransferase; CPT: diacylglycerol cholinephosphotransferase; MGAT: monoacylglycerol acyltransferase; SDP: suger-dependent protein; AGK: acylglycerol kinase; MGL: acylglycerol lipase; GLPK: glycerol kinase; PLA: phospholipase; LPCAT: lysophosphatidylcholine acyltransferase

Article Snippet: The KEGG pathway annotation (release 90.0) for the assembled transcriptome was performed at BGI-Shenzhen [ ].

Techniques: Expressing

Journal: PLOS ONE

Article Title: Biomarker combination predicting imminent relapse after discontinuation of biological drugs in patients with rheumatoid arthritis in remission

doi: 10.1371/journal.pone.0299450

Figure Lengend Snippet: a Protein–protein interaction (PPI) networks of 9 target proteins associated with late relapse shown in red were analyzed by STRING database with a confidence score of 0.4, and five more targets were identified and shown in yellow. Line thickness indicates the strength of data support. b Top 15 pathways from KEGG pathway analysis of 9 proteins associated with late relapse. X-axis indicates the significance (–log 10 [FDR]) of the pathway association, in bars. The PPI image was created using Cytoscape (ver. 3.9.1, https://cytoscape.org ). The image of pathway analysis was created using GraphPad Prism 9 ( www.graphpad.com ).

Article Snippet: The STRING functional enrichment outputs on the KEGG pathway were created using GraphPad Prism 9.

Techniques: