Dataset catalogue
Sources, measurements, and coverage recorded by starplast.datasets.REGISTRY.
This table is generated with python scripts/update_datasets.py. Coverage figures
refer to the registered source or cached build, not to every possible experiment.
The catalogue covers 128 registered datasets and computed layers across both organisms. Source links lead to the registered data download or original publication. GEO and PRIDE accessions also link to their archive records. Computed layers link to their input datasets; missing publication citations are marked explicitly. Raw source files are not all bundled with the Python package.
DNA — genetic perturbation and DNA-level readouts
| Dataset | Type of data | Coverage | Reference | Source |
|---|---|---|---|---|
| Arrayed splitCas9 imaging screen | What a parasite looks like when a gene is off: egress, actin, apicoplast, replication | 319 genes screened, 99 with a phenotype, 35 at egress | PMID 35538310; Nat Microbiol 41564-2022-01114 Supplementary Tables 2 and 3B | Source data |
| CRISPR screen at low and high parasite density | Fitness at low and high infection density, and which genes high density needs | 7,461 (91.7%) | Giuliano CJ, Kalluraya CA, Kloehn J, Sloan MA, Bunkofske ME, Hunter CA, Soldati-Favre D, Harding CR, Lourido S. Convergent evolution of metabolic regulation governs redox adaptation in Toxoplasma. Cell 2026 Aug, doi:10.1016/j.cell.2026.07.029; PMID 42580337; Cell 2026 Supplementary Table 1 (mmc2) | Source data |
| CRISPR screen without glucose or glutamine | Fitness on glucose alone, on glutamine alone, and which carbon source a gene needs | 7,393 (90.8%) | Uboldi AD et al., Differentiation of Toxoplasma into latent forms is linked to central carbon metabolism and requires a GID/CTLH-type E3 ligase. bioRxiv 2025, doi:10.1101/2025.07.27.667068 (preprint); bioRxiv 10.1101/2025.07.27.667068 Table S1 | Source data |
| Differentiation reporter CRISPR screen (COMPUTED) | Guide enrichment in reporter-positive parasites against the bulk population | 235 genes | GSE132237 | Source data |
| Fitness in the reporter strain (COMPUTED) | Guide depletion over eight passages of ordinary growth | 262 genes | GSE132237 | Source data |
| GRA12 strains and mouse subspecies | Median L2FC in vitro and in vivo, DISCO score; two screens | 236 / 232 | GRA12 is a common virulence factor across Toxoplasma gondii strains and mouse subspecies; PMID 40240328 | Source data |
| GRA17 synthetic-lethal screen | RH and RH-delta-gra17 phenotype by passage; MAGeCK p-values | 7,553 (genome-wide) | Genome-wide CRISPR screen identifies genes synthetically lethal with GRA17, a nutrient channel encoding gene in Toxoplasma; PMID 37498952 | Source data |
| HDAC3 occupancy (CUT&TAG, COMPUTED) | Mean HDAC3 CUT&TAG coverage over the promoter, relative to the genome mean | 8,140 genes (100%) | GSE277553 | Source data |
| Histone H4 acetylation (ChIP-chip, via ToxoDB) | Genome-wide H4 K5/K8/K12/K16 acetylation score within 1 kb of the gene | 7,515 genes (92%) | ToxoDB Hakimi/Ali H4 acetylation | Source data |
| Host ESCRT recruitment screen (UNPUBLISHED) | Per-gene effect on host TSG101 recruitment to the vacuole, by two models | 13 and 8 genes | Olafsson EB et al., A pooled image-based CRISPR screen identifies EAF1 as a T. gondii modulator of ESCRT subversion. bioRxiv 2026 (under submission); spaCR screen, bioRxiv 10.64898/2026.07.08.737057 | Source data |
| Host-transcription effector screen | Hotelling T2 plus full per-effector host-response signature | 252 screened / 22 full signatures | High-throughput identification of Toxoplasma gondii effector proteins that target host cell transcription; PMID 37827122 | Source data |
| In vitro CRISPR fitness (HFF) | Competitive growth in fibroblasts | 7,325 (90.0%) | A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes (Sidik et al. 2016); PMID 27594426 | Source data |
| In vitro evolution resistome and field variation | How often a gene mutated under compound selection, and whether the paper calls it a target | 735 selected / 4,941 field genes | Luth MR et al., Systematic in vitro evolution in Plasmodium falciparum reveals key determinants of drug resistance. Science 2024;386:eadk9893; PMID 39607932; Science Supplementary Data 3, 5, 6 | Source data |
| In vivo CRISPR composite scores | Differential fitness x significance in six mouse tissues after acute infection | 7,395 (90.8%) | Giuliano CJ et al., CRISPR-based functional profiling of the Toxoplasma gondii genome during acute murine infection. Nat Microbiol 2024;9:2323-2343; PMID 38977907; Nat Microbiol 2024 Supplementary Data 5, sheet Genome-Wide Differential | Source data |
| In vivo CRISPR platform | Mean log fold-change across replicates | 168 | A CRISPR platform for targeted in vivo screens identifies Toxoplasma gondii virulence factors in mice; PMID 31481656 | Source data |
| In-vivo fitness of hyperLOPIT-unassigned proteins | Two targeted libraries tested during mouse infection | measured at build time | Tachibana Y et al., CRISPR screens identify genes essential for in vivo virulence among proteins of hyperLOPIT-unassigned localization. mBio 2024; PMID 39082802; GSE253884;GSE253885 | Source data |
| Macrophage CRISPR screens | Naive BMDM and IFN-gamma survival | 7,402 (90.9%) | Wang Y et al., Genome-wide screens identify Toxoplasma gondii determinants of parasite fitness in IFN-gamma-activated murine macrophages. Nat Commun 2020;11:5258; PMID 33067458 | Source data |
| Male and female fertility, transferred from P. berghei | Whether a knockout loses male or female fertility, measured in the rodent parasite | 1,121 orthologs (19.6%) | Sayers C et al., Systematic screens for fertility genes essential for malaria parasite transmission reveal conserved aspects of sex in a divergent eukaryote. Cell Syst 2024;15:1075-1091.e6; PMID 39541984; Cell Systems Table S1 sheet A | Source data |
| Oxidative-stress CRISPR screen | Screening score per gene under oxidative challenge | 7,384 genes (91%) | PMID 34163449; PMC8216390 Data Sheet 1 | Source data |
| P. berghei knockout fitness, transferred to falciparum | Relative growth of berghei knockouts, carried onto their falciparum orthologs | 2,448 falciparum genes of 2,578 berghei mutants | PMID 28708996; Cell 2017 Table S1 (PlasmoGEM) | Source data |
| P. berghei liver-stage fitness, transferred to falciparum | How a berghei knockout fares through the liver, carried onto its falciparum ortholog | 754 falciparum genes; 180 reduced | PMID 31730853; Cell 2019 Table S2 (PlasmoGEM liver stage) | Source data |
| Plasmodium falciparum piggyBac saturation mutagenesis | Mutagenesis index and fitness score from a genome-saturating transposon screen | 5,720 P. falciparum genes | Zhang M et al. Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Science 2018; PMID 29724925; PlasmoDB GenesByTaxon attributesTabular | Source data |
| Promoter accessibility (ATAC-seq, COMPUTED) | Mean ATAC coverage over the promoter, relative to the genome mean | 7,988 genes (98%) | GSE313048 | Source data |
| Serum-restriction CRISPR screens (10% vs 1% FBS) | Fitness in lipid-rich and lipid-limited medium, and the lipid-dependence difference | 7,395 (90.8%) | Bitew MA et al., A genome-wide CRISPR screen identifies GRA38 as a key regulator of lipid homeostasis during Toxoplasma gondii adaptation to lipid-rich conditions. Nat Commun 2025;16:11177; PMID 41407671; Nat Commun 2025 Supplementary Data 2 (MOESM4) | Source data |
| Young 2019 in vivo screen | In vivo fitness | 115 | Young J et al., A CRISPR platform for targeted in vivo screens identifies Toxoplasma gondii virulence factors in mice. Nat Commun 2019;10:3963; PMID 31481656 | Source data |
Transcription — RNA abundance
| Dataset | Type of data | Coverage | Reference | Source |
|---|---|---|---|---|
| 5' UTR architecture from reannotated transcripts | Length, upstream AUGs and ORFs, and start-context strength of each 5' UTR | 5,992 (73.6%) | Peters ML et al., 5' untranslated regions tune Toxoplasma translation. bioRxiv 2025, doi:10.1101/2025.07.14.664749 (preprint); GSE302108 / bioRxiv 10.1101/2025.07.14.664749 Supplementary Data 4 | Source data |
| Alkaline-stress differentiation transcriptome | Unstressed tachyzoites and alkaline-stressed bradyzoites | 7,880 (96.8%) | Waldman BS et al., Identification of a Master Regulator of Differentiation in Toxoplasma. Cell 2020;180:359-372.e16; PMID 31955846; GSE132248 | Source data |
| Antisense transcription (via ToxoDB) | Percentile of antisense signal at this gene, across the life cycle | 8,140 genes (100%) | ToxoDB full life-cycle transcriptome, Antisense | Source data |
| BFD2-bound transcriptome (RIP-seq, COMPUTED) | Enrichment of each transcript in the BFD2 immunoprecipitation | 7,463 genes (92%) | GSE223620 | Source data |
| Bradyzoite restriction-checkpoint transcriptome | Cyclin perturbations in tachyzoite and bradyzoite conditions | measured at build time | GSE200962 | Source data |
| Bradyzoite subtypes in the mouse brain (single-cell) | Average expression in each of five subtypes of in vivo bradyzoite | 7,739 (95%) | Ulu A et al., Bradyzoite subtypes rule the crossroads of Toxoplasma development. Nat Commun 2026;17:1783; PMID 41580398; GSE311669 / Supplementary Data 1 | Source data |
| CPSF4 RNA-processing perturbation transcriptome | RNA response at 7, 24 and 48 hours after CPSF4 depletion | measured at build time | Farhat DC et al., A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity. eLife 2021;10:e68312; PMID 34263725; GSE168155 | Source data |
| Enteroepithelial stage transcriptome (via ToxoDB) | Expression in the feline enteroepithelial stages against tachyzoites | 7,739 genes (95%) | ToxoDB Ramakrishnan enteroepithelial | Source data |
| Expression in infected macrophages (via ToxoDB) | Expression percentile in ME49-infected murine macrophages | 8,140 genes (100%) | ToxoDB Saeij 29 strains | Source data |
| Feline merozoite transcriptome | Merozoite expression with matched tachyzoite comparators | measured at build time | Behnke MS et al., Toxoplasma gondii merozoite gene expression analysis with comparison to the life cycle. BMC Genomics 2014;15:350; PMID 24885521; GSE51780 | Source data |
| Genome-wide mRNA decay after actinomycin D | Wild-type mRNA remaining after 4 h of transcription block, relative to the median | 5,944 (73%) | Giuliano CJ et al., Convergent evolution of metabolic regulation governs redox adaptation in Toxoplasma. Cell 2026; PMID 42580337; GSE329845 | Source data |
| In vivo brain-stage transcriptome | Tachyzoites, acute/chronic whole brain, and purified bradyzoites | 7,663 (94.1%) | Garfoot AL et al., Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts. BMC Genomics 2019;20:859; PMID 31726967 | Source data |
| Life-cycle stage enrichment (DERIVED) | Which stage a gene's own expression is highest in | 1,911 of 8,140 genes called | citation not yet confirmed | Computed from Stage transcriptome; Oocyst sporulation series |
| MORC depletion and BFD1 perturbation transcriptome | MORC knockdown, BFD1 knockout and BFD1 stabilization series | 7,841 (96.3%) | PXD058095 | Source data |
| Novel transcript models (Nanopore, via ToxoDB) | How many novel TALON transcript models long reads support for this gene | 798 genes (10%) | ToxoDB Stuart/Ralph nanopore | Source data |
| Oocyst sporulation series | Unsporulated / sporulating / sporulated, 2 replicates (6 columns) | 7,974 (98.0%) | GSE206344 | Source data |
| Plasmodium falciparum life-stage and polysomal RNA | Transcript abundance across seven life stages, and what is on ribosomes | 5,720 P. falciparum genes | PlasmoDB: Su seven stages, Bunnik polysomal IDC, Gomez-Diaz mosquito stages | Source data |
| Plasmodium intraerythrocytic cycle timing | When in the 48-hour cycle each transcript peaks, and how strongly it cycles | 5,038 genes timed of 5,499; 461 do not cycle strongly enough to place | PMID 34668757; GSE163144 | Source data |
| Plasmodium long-read transcript models | Transcript models per gene, and how many the annotation does not contain | 1,857 genes, 2,498 models, 238 novel | PMID 40316999; Malar J 05376 Supplementary Data 2 | Source data |
| Plasmodium peak expression and stage label (DERIVED) | Maximum expression across stages, and which stage a gene belongs to | 5,720 genes for the maximum, 310 labelled | citation not yet confirmed | Computed from Plasmodium falciparum life-stage and polysomal RNA |
| Plasmodium transcription at febrile temperature | Wild type and two mutants at 37 C and at the 41 C of a malarial fever | 5,791 genes | PlasmoDB Pfal3D7 Febrile temps RNA-Seq | Source data |
| Plasmodium transcription under Sir2 knockout | Wild type and sir2a / sir2b knockout at ring, trophozoite and schizont | 5,615 genes | PlasmoDB Sir2 KO Marray | Source data |
| Primary brain-cell parasite differentiation time course | Parasite base mean and log2 fold-change at days 1, 2, 4, 7 and 14 | measured at build time | Mouveaux T et al., Primary brain cell infection by Toxoplasma gondii reveals spontaneous bradyzoite differentiation and modification of neuron biology; PMID 34610266; GSE168465 | Source data |
| Pru tachyzoite / 72-hour bradyzoite stage array | Matched tachyzoite and alkaline-induced bradyzoite expression | 7,253 genes | GSE22258 | Source data |
| Sexual development in the cat (single-cell atlas) | Enrichment at 8 days post-infection, when gametogony happens | 4,463 genes (55%) | Alrubaye HS et al., A single-cell atlas of Toxoplasma sexual development in the feline intestinal tract. Nat Microbiol 2026;11:1450-1462; PMID 42020723; PMC13042011 supplementary media-2 | Source data |
| Single-parasite transcriptional atlas (cell cycle) | Measured cell-cycle phase per gene, and pseudotime cluster | 873 genes phased, 7,499 clustered | Xue Y et al. eLife 2020;9:e54129; PMID 32065584 | Source data |
| Stage transcriptome | Tachyzoite, day 3/5/7, in vivo tissue cyst (12 columns) | 7,739 (95.1%) | GSE108740 | Source data |
| Synchronized tachyzoite cell-cycle transcriptome | Two replicates across blocked, asynchronous and hourly release states | measured at build time | Behnke MS et al., Coordinated progression through two subtranscriptomes underlies the tachyzoite cycle of Toxoplasma gondii. PLoS ONE 2010;5:e12354; PMID 20865045; GSE19092 | Source data |
| Transcription in a drug-tolerant latent state | Change in each gene in latent parasites, and the paper's 200-gene latency classifier | 4,887 genes (85%) | Aryal A et al., Environmental stress promotes entry into a pre-existing latent state in Plasmodium falciparum. bioRxiv 2026, doi:10.64898/2026.09.13.751295 (preprint); bioRxiv 10.64898/2026.09.13.751295 Supplementary Tables 7 and 24 | Source data |
| m6A methylation per transcript | How many canonical methylation sites a transcript has, and how fully methylated | 5,285 genes (92%) | Levendis JM et al., m6A positions polyadenylation in Plasmodium falciparum. bioRxiv 2026, doi:10.64898/2026.05.19.726191 (preprint); bioRxiv 10.64898/2026.05.19.726191 Supplementary Tables 6-8 | Source data |
| m6A methylome (MeRIP peaks) | How many m6A peaks the authors called on this gene in tachyzoites | 837 genes (10%) | PMID 34324585; PLoS Pathogens 1009335 Table S3A | Source data |
| mRNA stability after actinomycin D | Proportion of transcript remaining after five hours of transcription block | 412 genes | PMID 39899594; PLoS Pathogens 1012857 Table S12 | Source data |
| mRNA synthesis and decay rates through the blood-stage cycle | Transcripts made per minute, and transcripts lost per minute, at each gene's peak | 4,373 / 4,420 genes | Painter HJ, Chung NC, Sebastian A, Albert I, Storey JD, Llinas M. Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. Nat Commun 2018;9:2656; PMID 29985403; GSE66669 / Nat Commun Supplementary Data 2 | Source data |
Translation — protein abundance
| Dataset | Type of data | Coverage | Reference | Source |
|---|---|---|---|---|
| AP2XII-1/AP2XI-2 perturbation total proteome | Replicate abundance and log2 fold-change during pre-sexual conversion | 3,005 (36.9%) | Antunes AV et al., In vitro production of cat-restricted Toxoplasma pre-sexual stages. Nature 2024;625:366-376; PMID 38093015; PXD039400, PXD042658 | Source data |
| Blood-stage proteome and Hsp90 dependence | Protein abundance in a DMSO control, what two Hsp90 inhibitors do to it, and the paper's chaperone-dependent call | 3,049 proteins (53%) | Ibrasheva N et al., Chemoproteomic profiling of Plasmodium falciparum Hsp90 inhibition reveals functional link to DNA replication pathways. bioRxiv 2026, doi:10.64898/2026.08.28.747854 (preprint); PXD079493 / bioRxiv 10.64898/2026.08.28.747854 Tables S1-S2 | Source data |
| Co-translation layer (COMPUTED) | Gene pairs whose ribosome footprints covary | 6,231 edges over 7,437 genes | citation not yet confirmed | Computed from Intracellular/extracellular ribosome profiling; Host-context parasite ribosome profiling; Differentiation ribosome profiling (eIF1.2) |
| Differentiation ribosome profiling (eIF1.2) | RPF and RNA counts, and their ratio, in tachyzoites and pre-bradyzoites | 7,880 genes (97%) | PMID 38782906; GSE245775 | Source data |
| High-resolution ribosome profiling (5'UTR study) | Translation efficiency per replicate, footprints over matched RNA | 5,992 (73.6%) | Peters ML et al., 5' untranslated regions tune Toxoplasma translation. bioRxiv 2025, doi:10.1101/2025.07.14.664749 (preprint); GSE302107 | Source data |
| Host-context parasite ribosome profiling | Parasite ribosome footprints, RNA and translation efficiency in two HFF states | measured at build time | Holmes MJ et al., Simultaneous Ribosome Profiling of Human Host Cells Infected with Toxoplasma gondii. mSphere 2019;4:e00292-19; PMID 31167946; GSE129869 | Source data |
| Intracellular/extracellular ribosome profiling | Ribosome footprints, matched RNA and relative translation efficiency | measured at build time | Hassan MA et al., Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii. BMC Genomics 2017;18:961; PMID 29228904; GSE99395 | Source data |
| Mature gametocyte proteome and translatome | What a stage V gametocyte contains, and which proteins it is still making | 2,544 proteins (44%) | Alves E et al., The translatome of quiescent Plasmodium falciparum gametocytes reveals parasite pyridoxal kinase as a target. bioRxiv 2026, doi:10.64898/2026.03.24.713170 (preprint); PXD075878 / bioRxiv 10.64898/2026.03.24.713170 Extended Data Tables 1, 3 | Source data |
| Oocyst developmental-stage iTRAQ proteome | iTRAQ abundance ratios across oocyst developmental stages | 2,079 (25.5%) | Possenti A et al., Proteomic Differences between Developmental Stages of Toxoplasma gondii Revealed by iTRAQ-Based Quantitative Proteomics. Front Microbiol 2017;8:1732; PMID 28626452; PXD003765 | Source data |
| Plasmodium ribosome profiling across the asexual cycle | Ribosome-footprint and mRNA density per gene at five points of the blood-stage cycle | 3,501 genes (61%), 2,182 at the ring and 1,174 at the merozoite | PMID 25493618; GSE58402 | Source data |
| Protein melting temperature across the blood-stage cycle | The temperature at which each protein leaves solution in an intact cell | 2,039 proteins (35.6%) | Pazicky S et al., MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages. Nat Microbiol 2025;10:3229-3244; PMID 41315737; PXD056075 / Nat Microbiol Supplementary Table 1 | Source data |
| Proteome and transcriptome without iron | Change in each protein, and in each transcript, after 24 h of iron depletion | 5,047 protein / 3,113 RNA | Hanna JC et al., Global translational and metabolic remodeling during iron deprivation in Toxoplasma gondii. mBio 2026;17:e0378825; PMID 41925342; mBio Tables S1 and S2 | Source data |
| Proteome of sexually committed parasites | How much more or less of each protein a committed parasite carries | 1,950 proteins (34%) | Venugopal K et al., Defining the proteome of sexually committed parasites in Plasmodium falciparum. Mol Cell Proteomics 2026;25:101505; PMID 41482054; PXD059080 / MCP Table S3 | Source data |
| Pru proteome and IP abundance | Median log2 iBAQ across replicates | 748 (9.2%) | PXD043808, PXD065585 | Source data |
Post-translation — properties of the folded protein
| Dataset | Type of data | Coverage | Reference | Source |
|---|---|---|---|---|
| Antimalarial target engagement (thermal profiling) | How many of 25 antimalarials measurably engage each protein, and how many tested it | 3,126 proteins (55%) | Pazicky S et al., Thermal proteome profiling identifies new drug targets in Plasmodium falciparum parasites. bioRxiv 2026, doi:10.64898/2026.01.30.702724 (preprint); PXD048737-PXD048772 / bioRxiv 10.64898/2026.01.30.702724 Table S3 | Source data |
| BioID/TurboID supplement membership corpus | Number of downloaded proximity-labeling studies whose supplement names each gene | measured at build time | citation not yet confirmed | Source data |
| C. parvum hyperLOPIT | Donor labels for orthoLOPIT transfer | 1,107 usable | Guerin et al. 2023 | Source data |
| CDPK1 substrates (thiophosphate labelling) | Thiophosphorylated peptides per gene from analog-sensitive CDPK1 | 361 genes | PMID 37933960; eLife 85654 supplementary file 6 | Source data |
| Calcium thermal-shift proteome (mineCETSA) | How far a protein's melting curve moves when calcium is added | 2,348 proteins | PMID 35976251; PMC9436416 Supplementary file 3 | Source data |
| Chromatin-state proximity proteomes | How enriched each protein is near heterochromatin, active marks and the centromere | 2,020 proteins (35%) | Ramon-Zamorano G et al., Protein landscape of the chromatin states in the malaria parasite Plasmodium falciparum. bioRxiv 2025, doi:10.1101/2025.09.23.678001 (preprint); bioRxiv 10.1101/2025.09.23.678001 Tables S1, S5, S7 | Source data |
| Crosslinking MS interactome | How many proteins this one crosslinks to | 494 proteins | PMID 40874616; mBio 02159-25 supplementary file s0004 | Source data |
| Cyst wall interactome | Strongest bait signal and how many baits saw the protein | 56 proteins | PMID 32019789; PMC7002340 Data Set S1 | Source data |
| Foldseek structural similarity | TM-align over Toxoplasma AlphaFold models, TM >= 0.7 | 11,684 pairs / 2,338 genes | citation not yet confirmed | Computed from AlphaFold DB |
| Foldseek structural similarity (Plasmodium) | Which parasite proteins fold alike, without asking whether they are related | 4,571 pairs / 1,620 genes at TM >= 0.7 | citation not yet confirmed | Computed from Plasmodium model confidence and disorder (AlphaFold DB) |
| Host proteins at the vacuole | How enriched a host protein is at the parasitophorous vacuole | 12 host proteins | PMID 34898650; PLoS Pathogens 1010138 supplementary table | Source data |
| IP-MS of tagged baits | Replicated pulldown vs untagged control | 64 pairs / 48 genes | PXD043808, PXD065585 | Source data |
| IP-MS supplement membership corpus | Number of downloaded pulldown studies whose supplement names each gene | measured at build time | citation not yet confirmed | Source data |
| Local AlphaFold 3 protein models | sequence-verified AF3 confidence, coverage and confident-region geometry | 1,210 T. gondii genes with exactly matched local AF3 sequences | Einar Olafsson, unpublished local AF3 model collection (2026) | Source data |
| Lysine acetylome (GCN5b) | Acetylation sites reported per gene | 3,921 genes measured | PXD079431 | Source data |
| Lysine lactylome | Lactylation sites reported per gene | 515 genes measured | PXD031526 | Source data |
| MYR1 host interactome (bridge) | Host proteins co-immunoprecipitating with the parasite protein MYR1 | 219 host proteins, 1 parasite gene | PMID 32075880; PXD016383 | Source data |
| Monomethylarginine proteome (via ToxoDB) | Monomethylarginine sites reported per gene | 368 genes | ToxoDB Yakubu monomethylarginine | Source data |
| N-myristoylated proteome | The authors' confidence that this protein is myristoylated, 3 high to 1 low | 65 substrates | PMID 32618271; eLife 57861 supplementary file 4 | Source data |
| O-fucosylated glycoproteins (AAL pulldown) | Peptide identifications in the AAL lectin pulldown, per gene | 394 genes | PXD004426 | Source data |
| Oocyst-versus-tachyzoite phosphoproteome | Measured-site counts and strongest up/down phosphosite ratios | 1,603 (19.7%) | Wang Z-X et al., Comparative Phosphoproteomic Analysis of Sporulated Oocysts and Tachyzoites of Toxoplasma gondii Reveals Stage-Specific Patterns. Molecules 2022;27:1109; PMID 35164288; PXD017032 | Source data |
| Organelle-surface proximity proteomes | Enrichment near the cytosolic face of the apicoplast, mitochondrion and ER | 742 proteins | Parker KV, Huet D. A proximity biotinylation approach for the identification of membrane contact site proteins in Toxoplasma gondii. bioRxiv 2026, doi:10.64898/2026.08.05.743015 (preprint); bioRxiv 10.64898/2026.08.05.743015 Table S1 | Source data |
| P. falciparum LOPIT | Donor labels for orthoLOPIT transfer | 1,646 usable | Chisholm SA et al., The spatial proteome of the Plasmodium falciparum schizont. Nat Commun 2026;17:6192 -- CONFIRM against the file on disk; PMID 42218142 | Source data |
| PVM proximity labelling | Whether the study placed this protein at the parasitophorous vacuole membrane | 1,274 genes (73 positive) | PMID 34749525; mBio 00260-21 Data Set S1 | Source data |
| Phosphorylation under febrile heat stress | How far each protein's phosphorylation moves at 39 degrees, and at how many sites | 1,874 proteins (33%) | Jones D et al., Physiological febrile heat stress increases cytoadhesion through increased protein trafficking. Elife 2026;14:RP107860; PMID 42126964; PXD073843 / eLife Supplementary File 1 | Source data |
| Phosphosite counts | Count of phosphosites per protein, no positions | 1,175 (14.4%) | Treeck M et al. 2011 -- CONFIRM against the file on disk | Source data |
| Plasmodium CDPK1-dependent phosphosites | Phosphosites per gene that are lost when PfCDPK1 is knocked down | 62 genes, 73 sites | PMID 28680058; Nat Commun 00053 Supplementary Data 2a | Source data |
| Plasmodium N-myristoylome (NMT-inhibitor sensitive) | Proteins whose click-chemistry capture drops when N-myristoyltransferase is blocked | 16 substrates of 609 assayed | PMID 34695132; PLoS Biol 3001408 S11 | Source data |
| Plasmodium co-immunoprecipitation interactome (EPIC) | Which parasite proteins came down with each tagged bait, against its own control | 98 edges over 65 partners and 3 baits | PMID 28691708; Nat Commun 16044 Supplementary Tables 1-5 | Source data |
| Plasmodium extracellular vesicle proteome | Parasite proteins found in extracellular vesicles, and how many preparations found them | 184 proteins, 53 of them in both preparations | PMID 28944300; Wellcome Open Res 11910 S2 (PRIDE PXD006925) | Source data |
| Plasmodium lysine acetylome | Acetylated lysines per gene, and whether the gene was seen acetylated at all | 1,145 genes, 2,163 localised sites | PMID 26813983; Sci Rep 19722 S2 | Source data |
| Plasmodium lysine lactylome (resolved from NF54) | Lactylated lysines per gene, reported against NF54 and resolved to 3D7 | 144 genes | PMID 41417877; PLoS Genet 1011991 S1 | Source data |
| Plasmodium palmitome (observed only) | Proteins observed S-palmitoylated, with the motif prediction deliberately excluded | 503 proteins | PMID 36250062; Front Cell Infect Microbiol Table 3 | Source data |
| Plasmodium phosphosites (re-analysis of all public data) | Distinct phosphorylated residues per gene, pooled across every public study | 16,318 sites over 2,503 genes | PXD046874 | Source data |
| Protein melting temperature (mineCETSA) | Where this protein's melting curve sits, in degrees | 3,120 proteins (38%) | PMID 35976251; eLife 80336 supplementary file 3 | Source data |
| Proximity labelling | Proximity partners reported per gene | 1,734 genes measured | PXD059579 | Source data |
| Proximity-labeling corpus | 42 BioID/TurboID/APEX studies with a tagged Toxoplasma protein | 28 studies with data, 127 files | citation not yet confirmed | Source data |
| Pulldown corpus | 55 IP-MS / co-IP studies with a tagged Toxoplasma protein | 29 studies with data, 140 files | citation not yet confirmed | Source data |
| RNA-dependent proteins (R-DeeP) | Whether a protein's complex falls apart when the RNA is digested | 3,671 proteins (64%) | Hollin T et al., Proteome-wide identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes. Nat Commun 2024;15:1365; PMID 38355719; MassIVE MSV000091565 / Nat Commun Supplementary Data 1 | Source data |
| S-nitrosylation (iodoTMT) | S-nitrosylation sites reported per gene | 660 genes measured | PXD046083 | Source data |
| S-palmitoylome (Foe 2015, via ToxoDB) | 17-ODYA enrichment per gene, against hydroxylamine and against palmitate | 470 and 488 genes | PMID 26468752; ToxoDB Foe palmitome | Source data |
| Secreted-fraction partition | How a secreted protein splits between the soluble and vesicular fractions | 165 proteins | PMID 40874616; ToxoDB Ramirez-Flores vesicles | Source data |
| Spatial proteome of the schizont (hyperLOPIT) | Which of 24 cellular niches each protein sits in, and the classifier's confidence | 1,646 classified of 3,000 (29%) | Chisholm SA et al., The spatial proteome of the Plasmodium falciparum schizont illuminates the composition and evolutionary trajectories of its organelles. Nat Commun 2026;17:6192; PMID 42218142; PXD070842 / Nat Commun Supplementary Data 1 | Source data |
| StarPath crosslink MS | Measured physical proximity; residue-level crosslinks and Chai-1 complexes | 2,842 pairs / 1,630 genes | Mapping a Toxoplasma gondii interactome by crosslinking mass spectrometry and machine learning (2025); PMID 40874616 | Source data |
| T. gondii hyperLOPIT | Subcellular compartment, MAP and MCMC, with posteriors | 3,827 (47.0%) | A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT (Barylyuk et al. 2020); PMID 33053376 | Source data |
| Ubiquitination / SUMOylation (GlyGly) | GlyGly sites reported per gene | 128 genes measured | PXD042937 | Source data |
Reference — not a study result
| Dataset | Type of data | Coverage | Reference | Source |
|---|---|---|---|---|
| AlphaFold DB | Per-gene mean pLDDT; coordinates fetched on demand | 6,480 (79.6%) | Varadi et al. 2024 NAR (database); Jumper et al. 2021 Nature (method); UP000001529 (taxid 508771), AlphaFold DB | Source data |
| Antibody epitopes (IEDB) | Distinct antibody epitope sequences per gene | 34 genes, 222 distinct epitopes | IEDB bcell_search | Source data |
| Baseline mouse bone-marrow macrophage transcriptome | How much of each gene an unstimulated macrophage transcribes (TPM) | 15,437 mouse genes | John SV et al., Classically activated macrophages undergo functionally significant nucleotide metabolism remodelling driven by nitric oxide. Nat Metab 2025;7:1681-1702; PMID 40759751; GSE267544 | Source data |
| Codon usage bias (COMPUTED) | Effective number of codons, GC3, and codon adaptation index | 8,140 genes (100%) | ToxoDB ME49 | Source data |
| Drug sensitivity per gene (CURATED) | Knockouts with a measured shift in sensitivity to a named compound | 3 genes, 2 compounds | PMID 41025776; mBio, PMID 41025776 | Source data |
| Enteric / sexual-cycle fitness per gene (CURATED) | Gene disruptions carried through the feline stage with oocyst output measured | 8 genes, 4 studies | PMID 28288194; PMIDs 28288194, 30728393, 36809045 and PMC12942651 | Source data |
| Enzyme classification (ToxoDB) | EC number per gene, and whether it has one | 1,313 enzymes of 8,140 genes | ToxoDB ME49 | Source data |
| FANTOM5 mouse brain and skeletal muscle | How much of each gene the mouse tissues a bradyzoite persists in transcribe | 13,739 mouse genes; brain 9,763, skeletal muscle 8,635 | PMID 24670764; E-MTAB-3579 | Source data |
| Frozen ESM-2 protein representations | 320 sequence representation coordinates in a separate gene-keyed feature table | 8,064 T. gondii genes with valid bundled CDS translations | Lin et al., Science (2023); frozen ESM-2 8M model, local sequence encoding | Source data |
| GTEx median expression in two host cell types | How much of each gene the host cell transcribes, in the cell each parasite lives in | 19,087 human genes over 2 tissues | PMID 32913098; GTEx v10 | Source data |
| Host genes required for rhoptry discharge | Whether knocking out a human gene stops Toxoplasma discharging its rhoptries | 18,739 human genes | Valleau D et al., Clustering of host N-glycans licenses Toxoplasma rhoptry discharge. bioRxiv 2025, doi:10.1101/2025.10.16.682961 (preprint); bioRxiv 10.1101/2025.10.16.682961 v2 Table S1 | Source data |
| Human fibroblast response to Toxoplasma infection | Infected against uninfected HFF, per host gene: moderated log2 change and FDR | 10,631 human genes | GSE335016 | Source data |
| Human hepatocyte response to P. falciparum | Infected against uninfected primary hepatocytes, per host gene: log2 change and FDR | 12,550 human genes | Kanyal A et al., Inhibition of Wnt signaling in primary human hepatocytes promotes Plasmodium falciparum liver stage development. PLoS Pathog 2025;21:e1013800; PMID 41428747; GSE263643 | Source data |
| Human red blood cell SURFACE proteome, by population | Which host proteins are reachable from outside the cell the merozoite invades | 267 plasma-membrane proteins, 230 in both populations | PMID 31552303; Commun Biol 0596 Supplementary Data 2A | Source data |
| Human red blood cell proteome, by fraction | Which human proteins are present in the cell the blood stage lives in | 5,264 human proteins: 4,777 membrane, 2,350 cytoplasmic | PMID 41654503; Sci Data 06792 Supplementary Table S1 | Source data |
| IEDB epitopes mapped to genes (via ToxoDB) | How many IEDB epitopes ToxoDB maps to this gene | 221 genes | ToxoDB / IEDB | Source data |
| InterPro domains | Domain identity and count | 8,140 | citation not yet confirmed | Source data |
| Membrane lipid composition of parasite vesicles | Lipid species abundance, and its proportion against the host cell | 194 lipid species | PMID 41716462; Front Cell Infect Microbiol 1745625 Tables 1-3 | Source data |
| Metabolome and isotope labelling under iron deprivation | Steady-state metabolite levels and the fraction labelled from glucose or glutamine | 1,102 metabolites | PMID 41925342; mBio 03788-25 Tables S3 and S5 | Source data |
| Mouse bone-marrow macrophage cell-surface repertoire | Which host proteins are EXPOSED on the surface of the macrophage a tachyzoite invades | 1,296 mouse surface proteins, 150 of them on primary BMDM | PMID 25894527; PLoS ONE 0121314 S1 File | Source data |
| OrthoMCL orthogroups | Orthogroup assignment and cross-species bridge | 16,793 groups | OrthoMCL release 6.21 | Source data |
| PlasmoDB gene identity | Symbols, previous IDs, product descriptions for the Plasmodium arm | 5,791 P. falciparum 3D7 transcripts | PlasmoDB 3D7 | Source data |
| Plasmodium T-cell epitopes (IEDB) | Distinct T-cell epitope sequences per gene | 44 antigens, 1,542 distinct epitopes | IEDB tcell_search | Source data |
| Plasmodium antibody epitopes (IEDB) | Distinct antibody epitope sequences per gene | 434 antigens, 7,366 distinct epitopes | IEDB bcell_search | Source data |
| Plasmodium codon usage (COMPUTED) | Effective number of codons, GC3, and CAI against the ribosomal proteins | 5,318 genes | PlasmoDB-68 Pfalciparum3D7 AnnotatedCDSs | Source data |
| Plasmodium complexes from crosslinking MS | Which crosslink-derived complex a gene belongs to, and whether it reaches the host | 128 genes in 42 complexes | PMID 41966402; Cell Rep mmc5 Clusters | Source data |
| Plasmodium crosslinking MS contacts | Protein pairs joined by a measured crosslink | 79 parasite-parasite pairs | PMID 41966402; Cell Rep mmc1 sheet D | Source data |
| Plasmodium enzyme classification (PlasmoDB) | EC number per gene, curated and orthology-derived kept apart | 1,220 curated, 335 more from orthology | PlasmoDB ecnumbers and ecnumbers_derived | Source data |
| Plasmodium export prediction (ExportPred) | Predicted export to the erythrocyte, as an ordinal confidence tier | 440 genes called at some threshold, 191 at the default | PlasmoDB GenesByExportPrediction | Source data |
| Plasmodium falciparum 3D7 InterPro domains | InterPro and Pfam domain content from the same PlasmoDB report | 5,720 P. falciparum genes | PlasmoDB GenesByTaxon attributesTabular | Source data |
| Plasmodium falciparum 3D7 gene attributes | The second species: gene structure and the protein's sequence properties | 5,720 P. falciparum genes | PlasmoDB GenesByTaxon attributesTabular | Source data |
| Plasmodium falciparum 3D7 orthology and paralogy | OrthoMCL group, ortholog and paralog counts from the same PlasmoDB report | 5,720 P. falciparum genes | PlasmoDB GenesByTaxon attributesTabular | Source data |
| Plasmodium falciparum abstract corpus (COMPUTED layer) | Who is named in the malaria literature, how deeply, and which genes appear together | 43,482 abstracts; 732 genes named in the first 10,000 | PubMed | Source data |
| Plasmodium falciparum strain variation | SNP counts across sequenced strains, from the same PlasmoDB report | 5,720 P. falciparum genes | PlasmoDB GenesByTaxon attributesTabular | Source data |
| Plasmodium host interaction degree (COMPUTED) | How many host proteins a gene was crosslinked to, where it was looked at | 117 genes seen, 10 with a host partner | citation not yet confirmed | Computed from Plasmodium to human contacts (crosslinking MS) |
| Plasmodium model confidence and disorder (AlphaFold DB) | Mean pLDDT per protein, and the fraction of it at each confidence band | 5,098 of 5,720 genes | AlphaFold DB API, per UniProt accession | Source data |
| Plasmodium relation layers (COMPUTED) | Gene pairs sharing an orthogroup or a domain, and pairs whose stages covary | 1,741 + 24,123 + 63,158 pairs | citation not yet confirmed | Computed from Plasmodium falciparum 3D7 orthology and paralogy; Plasmodium falciparum 3D7 InterPro domains; Plasmodium falciparum life-stage and polysomal RNA |
| Plasmodium to human contacts (crosslinking MS) | Parasite protein to erythrocyte protein, measured as a crosslink | 10 pairs, 10 parasite genes, 7 human proteins | PMID 41966402; Cell Rep mmc1 sheet D | Source data |
| Population and between-species variation per gene | Non-synonymous variation in field isolates, and dN/dS against Plasmodium orthologs | 4,282-5,232 genes | Chisholm SA et al., The spatial proteome of the Plasmodium falciparum schizont illuminates the composition and evolutionary trajectories of its organelles. Nat Commun 2026;17:6192; PMID 42218142; Nat Commun Supplementary Data 3 | Source data |
| PubMed Central open-access full texts | Sectioned JATS XML | 6,667 articles | citation not yet confirmed | Source data |
| PubMed abstracts | Titles and abstracts for co-mention and attention | 33,924 records | citation not yet confirmed | Source data |
| Strain variation (ToxoDB HTS SNPs) | SNPs per gene across every sequenced strain, split by effect | 8,140 genes (100%) | ToxoDB ME49 | Source data |
| ToxoDB gene identity | Symbols, previous IDs, product descriptions | 8,843 ME49 genes | ToxoDB ME49 | Source data |
| Validated resistance-conferring mutations (CURATED) | Mutations shown to CAUSE drug resistance by putting them back into a clean background | 1 gene, 3 substitutions, 3 compounds | PMID 24533298; Int J Parasitol Drugs Drug Resist, PMIDs 24533298 and 25941623 | Source data |