「pathway」の検索結果

Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways. Two-host architecture: api.clinpgx.org for annotation records, api.cpicpgx.org for genotype→recommendation lookups. No auth. For germline pathogenicity use clinvar-database; for somatic cancer PGx use cosmic-database or opentargets-database; for drug bioactivity use chembl-database-bioactivity.

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Ensembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs (HGNC, RefSeq, UniProt), regulatory features. For bulk local use pyensembl; for pathways use kegg-database.

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KEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/conv/link/ddi). ID conversion (NCBI/UniProt/PubChem). Use bioservices for multi-DB Python.

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GSEA and over-representation analysis (ORA) for RNA-seq and proteomics. Wraps Enrichr for ORA against MSigDB, KEGG, GO, and 200+ databases; runs preranked GSEA on ranked DE gene lists. Outputs enrichment tables and running-score plots. Use after DESeq2 or edgeR for pathway-level interpretation.

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Unified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI. For deep single-DB queries use dedicated tools (gget for Ensembl, pubchempy for PubChem); bioservices excels at cross-database workflows.

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Query STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species). Retrieve networks, run GO/KEGG enrichment, find partners, test PPI significance, visualize networks, analyze homology. For chemical interactions use chembl-database-bioactivity; pathways use kegg-database.

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Infer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts → subset CellChatDB ligand-receptor pairs → over-expressed genes per group → communication probabilities → pathway signaling → network centrality (senders/receivers/influencers) → chord/heatmap/bubble plots → cross-condition compare. Human, mouse. Use liana for pure-Python.

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Designing scientific schematics, diagrams, and graphical abstracts. Covers tool selection (BioRender, Inkscape, Affinity, PowerPoint), design principles for pathway diagrams, mechanism schematics, experimental workflows, and journal graphical abstracts. Includes composition, icon sourcing, color for biological entities, and accessibility. Use when creating illustrative (not data-driven) scientific figures.

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MaxQuant + Perseus proteomics pipeline: run MaxQuant for LFQ and SILAC; parse proteinGroups.txt in Python; filter contaminants/decoys; log2 + median-normalize; impute MNAR; t-test with FDR; volcano plot; GO/pathway enrichment. Use Proteome Discoverer for Thermo-native processing; FragPipe/MSFragger for GPU-accelerated DB search.

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Content web architecture framework. Use when diagnosing offer doc usage, content-to-conversion pathways, or why someone isn't getting sales despite traffic.

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Think and work like an expert Medical Geneticist. Use when a task calls for Medical Geneticist judgment. Reasons from pedigree priors, HPO phenotype match, and ACMG/ClinGen variant classification; integrates exome/genome, CMA, RNA splicing, NBS ACT pathways, Tier 3 carrier screening, SF v3.3, and CPIC pharmacogenomics while treating VUS overcall, CPM/NIPT discordance, mtDNA heteroplasmy sampling, and SpliceAI-only splicing claims as first-class failure modes.

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Think and work like an expert Metabolomics Scientist. Use when a task calls for Metabolomics Scientist judgment. Reasons from MSI annotation levels, pooled-QC RSD and D-ratio gates, MZmine/MS-DIAL/XCMS pipelines, HMDB/GNPS identification, and MetaboAnalyst batch correction (ComBat, QC-RLSC); treats injection-order drift, ComBat over-correction, and Level-5 pathway stories as first-class failure modes.

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Think and work like an expert Environmental Health Scientist. Use when a task calls for Environmental Health Scientist judgment. Reasons from source–pathway–receptor chains, classical vs Berkson exposure error, and tiered biomonitoring (NHANES/BEs); runs STROBE-grade epi, IRIS/OEHHA/ATSDR risk assessment, AERMOD/CALPUFF, EPHT/EJSCREEN, and HIA while treating surrogate misclassification, mobility bias, and detection≠harm as first-class failure modes.

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Think and work like an expert Environmental Chemist. Use when a task calls for Environmental Chemist judgment. Reasons from thermodynamic partitioning (K_oc/K_ow, Henry's law), pathway-specific half-lives, and mass balance through GC-MS/LC-MS/MS/ICP-MS analysis, EPI Suite and fugacity fate models, and EPA SW-846 QA/QC while treating blank contamination, matrix suppression, censored sub-LOD data, and unscoped transformation products as first-class failure modes.

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Think and work like an expert Environmental Engineer. Use when a task calls for Environmental Engineer judgment. Reasons from mass balances, reaction kinetics, source-pathway-receptor transport, and permit limits through BioWin/GPS-X, SWMM, AERMOD/CALPUFF, GAC/IX and activated-sludge design, and 40 CFR Part 136 QA/QC, while treating nitrifier washout, clarifier upset, PFAS breakthrough, and remediation rebound as first-class failure modes.

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Think and work like an expert Environmental Scientist. Use when a task calls for Environmental Scientist judgment. Reasons from source-pathway-receptor linkages, multimedia partitioning, and dose-as-exposure through conceptual site models, fate models (MODFLOW/MT3DMS, AERMOD), SW-846 QA/QC chains, and ProUCL/Mann-Kendall statistics while treating censoring bias, conceptual-model error, well-construction artifacts, and seasonal confounding as first-class failure modes.

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Think and work like an expert Comparative Medicine Researcher. Use when a task calls for Comparative Medicine Researcher judgment. Reasons from species biology, translational validity, and the 3Rs through model-validity frameworks, IACUC protocols, ARRIVE 2.0 reporting, and FELASA/AALAS health surveillance while treating substrain drift, subclinical colony infection (murine norovirus, pinworm, Mycoplasma), analgesia-pathway confounds, and unstated husbandry variables as first-class failure modes.

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Think and work like an expert Climate Risk Analyst. Use when a task calls for Climate Risk Analyst judgment. Reasons from TCFD/IFRS S2 four-pillar disclosure, NGFS Phase V orderly/disorderly/hot-house scenarios, hazard–exposure–vulnerability and RMS/AIR/CLIMADA cat economics, transition carbon-price and stranded-asset pathways, and PCAF financed emissions while treating exposure geocoding quality, Kotz damage-function retraction, and scenario-not-forecast misuse as first-class failure modes.

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Think and work like an expert Cell Signaling Biologist. Use when a task calls for Cell Signaling Biologist judgment. Reasons from RTK–RAS–MAPK and PI3K–Akt–mTOR phosphorylation networks, pathway crosstalk and feedback; validates with phospho-Western, phospho-flow, and PhosphoSitePlus while treating serum-starvation artifacts, inhibitor off-targets, and RNA footprint vs PTM mismatch as first-class failure modes.

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Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results. Covers dotplot, barplot, cnetplot, emapplot, gseaplot2, ridgeplot, and treeplot.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Cell Reports 36:109597), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Workflow for untargeted or targeted metabolomics including preprocessing, normalization, annotation, statistics, and pathway mapping.

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Routes between five assessment pathways — formative, rubric/criteria, authentic/performance, peer/self, and diagnostic — with validity and equity checks. Use when a teacher needs help choosing how to assess.

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Use when interpreting biological research findings, evaluating life science evidence, analyzing molecular or cellular mechanisms, comparing competing biological hypotheses, designing or critiquing experiments in biology, genetics, genomics, cell biology, immunology, neuroscience, ecology, or any life science domain. Triggers on questions about gene function, pathways, phenotypes, GWAS hits, single-cell data, animal models, clinical translation, evolutionary arguments, or any biology/life science reasoning task.

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