Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 27

System / cell line: prediction ✕ Assay: subcellular ✕ Clear

In Silico screening for functional candidates amongst hypothetical proteins.

PMID 19754976 · PMC2758874 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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An in silico selection strategy combining subcellular targeting-signal prediction with protein domain identification can enrich for true functional proteins among hypothetical proteins

hypothetical targetp-selected mitochondria-predicted subcellular domain database
pTARGET: a web server for predicting protein subcellular localization.

PMID 16844995 · PMC1538910 · Nucleic acids research · 2006 · 7 claims · 3 setups

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pTARGET web server predicts nine distinct subcellular localizations in eukaryotic non-plant proteins using an algorithm based on location-specific Pfam domain occurrence patterns and amino acid composition (AAC)

eukaryotic complete pfam amino subcellular
MitoP2: the mitochondrial proteome database--now including mouse data.

PMID 16381964 · PMC1347489 · Nucleic acids research · 2006 · 8 claims · 8 setups

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MitoP2 is a database integrating manually annotated mitochondrial reference proteins, functions, and disease associations for yeast, human, and mouse, with cross-species orthologue mapping

saccharomyces yeast heart liver genome-wide single transcriptome
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

PMID 15608166 · PMC540074 · Nucleic acids research · 2005 · 7 claims · 4 setups

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PA-GOSUB significantly extends the coverage of GO molecular function and subcellular localization annotations for 10 model organism proteomes compared with existing databases (GOA, Swiss-Prot).

sequences query swiss-prot naive-bayes blast feature
LOCATE: a mammalian protein subcellular localization database.

PMID 17986452 · PMC2238969 · Nucleic acids research · 2008 · 8 claims · 6 setups

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LOCATE is a curated, web-accessible database housing membrane organization and subcellular localization data for mouse and human proteins.

hela proteome indirect automated computational
Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups

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Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.

orthologues nih-3t3 3t3 mefs bioinformatic egfp co-transfection
Aggregation propensity of the human proteome.

PMID 18927604 · PMC2557143 · PLoS computational biology · 2008 · 8 claims · 7 setups

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Long proteins have, on average, less intense/pronounced aggregation peaks than short proteins

proteome non-membrane proteins membrane sequence-based correlation statistical
The malaria secretome: from algorithms to essential function in blood stage infection.

PMID 18551176 · PMC2408878 · PLoS pathogens · 2008 · 8 claims · 5 setups

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An expanded secretome (van Ooij secretome) built from a revised SignalP MaxS cutoff (0.571) plus HMMER-expanded HT-motif search yields 422 proteins (224 excluding RIFIN/STEVOR families).

falciparum berghei plasmodium signal comparative piggybac
Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

PMID 16162288 · PMC1261261 · BMC genomics · 2005 · 8 claims · 5 setups

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A novel rTS protein isoform, rTSγ, exists with a 27-residue longer N-terminus generated from an alternative upstream start codon relative to rTSβ.

rts rtsβ ccrf-cem comparative mitochondrial subcellular
Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

PMID 18267298 · PMC5054205 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 5 setups

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Out of 20 amino acids, the metabolic pathways of 17 utilize mitochondrial enzymes, and dysfunction of these enzymes causes over 40 known human mitochondrial diseases/disorders

mitoproteome orthologous liver mitochondrial sequence-based computational literature
Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

PMID 19930686 · PMC3091328 · Genome biology · 2009 · 8 claims · 6 setups

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The human mitochondrial proteome expanded via two prevailing gene duplication modes: intra-mitochondrial and inter-compartmental duplication

cerevisiae mitocarta mitochondrial tissues comparative subcellular gene
A global database for modeling tumor-immune cell communication.

PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups

Has reproduction · 66

TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures

pubmed scrna-seq tcga basal manual scrna-seq bulk
Phosphoproteomics: new insights into cellular signaling.

PMID 16168091 · PMC1242200 · Genome biology · 2005 · 8 claims · 8 setups

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Protein kinases are one of the largest gene families in humans and mice, accounting for 1.7% of the human genome

yeast hela beta2-adrenergic erk phosphopeptide targeted silac
Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

PMID 34745063 · PMC8564382 · Frontiers in microbiology · 2021 · 7 claims · 7 setups

Has reproduction · 67

Tn-seq using the TnSC189 mariner transposon identified 329 essential genes in V. anguillarum NB10Sm from a library of 52,662 insertion mutants.

vibrio coli anguillarum transposon-insertion conjugative functional
Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

PMID 15287975 · PMC507878 · Genome biology · 2004 · 8 claims · 6 setups

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3,848 Arabidopsis proteins were identified as likely plant-specific based on phylogenetic profiling and EST confirmation in multiple plant species

arabidopsis phylogenetic tblastn subcellular
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
Human protein reference database--2006 update.

PMID 16381900 · PMC1347503 · Nucleic acids research · 2006 · 7 claims · 6 setups

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HPRD is a comprehensive, continually expanded resource cataloging human protein domains, PTMs, protein-protein interactions, and other annotations.

proteins hela nucleolus signaling literature mass subcellular
Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 78

73 IQD gene family members (TaIQD1-73) were identified in the wheat genome and phylogenetically divided into six major groups.

triticum taiqd wheat promoter genome-wide phylogenetic synteny
Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.

PMID 36253367 · PMC9576764 · Nature communications · 2022 · 8 claims · 4 setups

Has reproduction · 100

The P. magna mitoribosome contains rRNA split into 13 fragments (LSU1-8, SSU1-4, mt-5S)

mitoribosome polytomella cross-species single-particle novo comparative
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular

Experiments

In Silico screening for functional candidates amongst hypothetical proteins.

pTARGET: a web server for predicting protein subcellular localization.

MitoP2: the mitochondrial proteome database--now including mouse data.

PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

LOCATE: a mammalian protein subcellular localization database.

Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

Aggregation propensity of the human proteome.

The malaria secretome: from algorithms to essential function in blood stage infection.

Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

A global database for modeling tumor-immune cell communication.

Phosphoproteomics: new insights into cellular signaling.

Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

Human protein reference database--2006 update.

Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.