Description of fields:
| Human synonyms | Symbols from NCBI at the time of MitoCarta2.0 creation | |
| Mouse ortholog | Mouse ortholog determined by BLASTP reciprocal best hit (Expect<0.001); Symbols from NCBI | |
| MoothaLab Resources | ||
| Coexpression | Coexpression across mouse tissue atlases (RNA atlas GNFv3, protein atlas Geiger, Mol. Cell Proteomics, 2013) [Note links will not be available if no mouse ortholog exists]. | |
| CCLE | Cancer Cell Line Encyclopedia of ~1000 cancer cell lines with RNA-seq and 391 cell lines with CRISPR screen data. | |
| Sequence alignment | (MitoCarta genes only) shows MUSCLE alignment for best bidirectional hits (BBH) for all 138 species, or for a pre-selected subset of 24 model organisms. Note TMHMM transmembrane domains are shown (black) as well as PFAM domains (blue) for each species | |
| MitoCarta3.0 | ||
| MitoCarta3.0 evidence | Listed features have log-odds score>1 (+ indicates logodds>5; ++ indicates score>7) | |
| MitoCarta2.0 FDR | Corrected false discovery rate for genes scoring this level or higher. MitoCarta2.0 list contains genes with cFDR<=5% or with Tmito curation | |
| MitoCarta2.0 Training | Curation of this gene as Tmito (definite mito), Tpossible_mito, or Tnon_mito. T stands for training data.' | |
| TargetP | TargetP confidence: TargetP confidence score (1-5, 1 is most confident) of mitochondrial targeting signal. Score 0 indicates no mitochondrial prediction | |
| MitoDomain | indicates protein has a PFAM domain that is exclusively mito (MitoDomain), exclusively non-mito (NonMitoDomain), or in both mito and non-mito proteins (SharedDomain), or no info (NoDomain). Uses swissprot annotations of PFAM domain and cellular loc across all eukaryotes. | |
| Yeast Homolog | OrthologMitoHighConf (HomologMitoHighConf) if yeast ortholog (homolog) is annotated mitochondrial in SGD with high confidence; OrthologMitoLowConf (HomologMitoLowConf) if yeast ortholog (homolog) is annotated mitochondrial in SGD with low confidence (dual localized or only based on high throughput data), NoMitoHomolog indicates no yeast homolog or homolog is not annotated mitochondrial in SGD. | |
| Rickettsia Homolog | Rickettsia Homolog: Ortholog if 1:1 ortholog between mouse and Rickettsia prowazekii; Homolog if homology between mouse and Rickettsia prowazekii, otherwise NoHomolog. | |
| GeneAtlas Coexpression N50 | N50 score for coexpression across mouse GNFv3 tissue atlas (N50 = number of 50 nearest neighbors that are in Tmito). | |
| PGC Induction | Foldchange in transcript induction following overexpression of PGC1a, known to induce mitochondrial biogenesis. | |
| MSMS score | Category indicating MS/MS abundance (coverage) and enrichment in subtractive proteomics (either pure-enriched, crude-enriched, or ambiguous). | |
| MSMS intensity | log10 intensity in each tissue. cer=cerebrum, cbl=cerebellum, bra=brainstem, spi=spinalcord, kid=kidney, liv=liver, hea=heart, skm=skeletalmuscle, adi=adipose, smi=smallintestine, lgi=largeintestine, sto=stomach, pla=placenta, tes=testis | |
| Mootha Lab CRISPR Screen Results | ||
| GluGalDeathScreen (2016) | Arroyo et al, Cell Metabolism 2016; Three possibilities: General growth defect; Enriched in Gal/Glu dead cells (fdr < 0.10) (and not General growth defect); not significantly enriched in Gal/Glu dead cells (fdr > 0.10) | |
| O2_screen_summary (2020) | Jain et al, Cell 2020. Selectively essential in 1% vs 21% oxygen (day 15), with fdr | |
| 1%O2_vs_21%O2.day15.score (2020) | Zscore for 1% vs 21% oxygen on day 15 | |
| 21%O2.day15_vs_day0.score (2020) | Zscore for abundance at day 15 vs day 0 (21% oxygen) | |
| Chemical genetics Zscore (To 2019) | To et al, Cell 2019 Chemical Genetic Screen: significant hits (FDR<0.10) reported for the following drugs: DMSO, Metformin (Met), Piericidin (Pier), Antimycin (Anti), Oligomycin (Olig), Antimycin + Oligomycin (AO), ethidium bromide (Etbr), and chloromphenicol (CAP). Negative Z scores indicate lower growth in the condition, positive scores indicate higher growth in the condition. | |
| TMRM_Oligo_Zscore | TL's unpublished 'set point assay' data: enriched in the low sorted tail of TMRM distribution under oligomycin | |
| RefSeq Protein Isoforms | ||
| TargetP (v1.0) | TargetP version 1 was run and predicted either signal peptide (S), mito targeting signal (MTS), or no prediction. Confidence score (conf) between 1 (high conf) and 5 (low conf). If MTS is predicted, the predicted MTS length is provided (note confidence score is only presence of MTS and not confidence of its length). Eg 'MTS (conf=1 len=22)' indicates a high confidence MTS, with length predicted at 22. | |
| TargetP (v2.0) | TargetP version 2 was run and predicted either signal peptide (SP), mito targeting signal (MTS), or no target prediction (noTP). Score indicates likelihood (higher is better) and length is the predicted MTS length | |
| TPpred2 | TPpred2 was run, and indicates score and predicted length of MTS | |
| MitoFates MTS Len | MitoFates was run in 2016 for paper PMID: 28122942, and if an MTS was predicted, the lengths of all predicted MTS are listed | |
| Mouse Best | Best cleavage for this mouse protein based on PMID:28122942 which integrates experimental data (N-terminal mito proteomics of isolated mouse liver and kidney), with predictions to provide the best supported MTS length (for one mouse protein per gene). Not provided for human proteins since data was generated only for mouse. | |
General: the previous MitoWiki website was not supported and failed. This previous website had user sign-in, manual annotation of gene function and disease status, as was as static information of mito-relevant data per protein. This new website just as the static information, without a wiki ability to manually update entries.