First-pass data types explained

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Current First Pass Curator form

"flagged" = WBPapers that have been flagged for that particular data type but not curated yet or not assessed for curation status yet; "flagged-done" = WBPapers that have been flagged and curated. These papers can be used as a source for verified curation flag examples.

Automatation status Data type Description Examples of info sent to data curator Curator Flagged
Gene Symbol (main/other/sequence) Genes studied in this paper (flagged-done): New symbol for known locus or new locus defined. Alerts curators to newly cloned genes so that they can update a previously existing concise description, if needed. "UNC-80 = F25C8.3"; "We refer to the long F59F5.2/.8 transcript as glo-3 and the F59F5.2 transcript as glo-3 short (Figure 5A)."; "tbc-1=F20D1.2 table S3"; "nre-1 (uncloned)"; "we have designated K02B9.1 as meg-1 and K02B9.2 as meg-2 (meg, maternal-effect germ-cell defective).",
Mapping Data Genetic mapping data (flagged): 3-factor interval mapping-genetic only, no SNP interval mapping; mapping with Df, breakpoints, Dp "in suppl: In three-factor mapping with unc-11(e47) dpy-5(e61) the...defect mapped between the two genes (9/16 Dpy non-Unc and 4/14 Unc non-Dpy were chemotaxis defective)"; "glo- 3(kx90), glo-3(kx94), and glo-3(zu446) were complemented by nDf19...similar to nearby genes vab-3 and daf-12"; "fig.1 ...breakpoint was not mapped precisely but idDf3 completely removes sequences of fem-1, drp-1..."; "mapping data in suppl methods: We mapped sa321 by its daf-7 suppression phenotype to the unc-62 dpy-11 interval (unc-62 (4/10) sa321 (6/10) dpy-11), which excludes scd-2. Therefore, sa321 is not allelic with scd-2."
Gene Function Gene function (flagged-done): Discussion of new function of a gene "A Novel Role for the SMG-1 Kinase in Lifespan and Oxidative Stress Resistance in Caenorhabditis elegans"; "Here we describe the isolation of mutations in two adjacent, divergently transcribed open reading frames (eri-6 and eri-7) that fail to complement...The ERI-6/7 protein is a superfamily I helicase that both negatively regulates the exogenous RNAi pathway and functions in an endogenous RNAi pathway."
in progress Gene Regulation on Expression Level Altered gene expression (flagged-done): Gene expression level change in genetic background, ie, gfp expression (or any other reporter) increases or decrease; expression level change under certain chemical/physical conditions, ie, drugs, heat shock, etc.; expression location change in genetic background, missexpression, ie, nucleus, cytoplasma, etc.; no change in gene expression in genetic background if mentioned in paper. Basically, paper reports changes or lack of changes in gene expression level or pattern due to genetic background, chemical, temperature or other experimental treatment. "Figure 5. Loss of hcf-1 Promotes the DAF-16 Transcriptional Regulation of Several Target Genes"; "To investigate whether SMG-1 controls DAF-16 sub-cellular localization...DAF-16::GFP was localized in both the cytoplasm and the nucleus in all tissues of worms after smg-1 inactivation...(Figure 3)...daf-2 RNAi induced DAF-16::GFP nuclear accumulation (Figure 3)...SMG-1 does not regulate DAF-16 activity through its sequestration into the cytoplasm"; "Interestingly, the eri-6/7 transsplicing reporter is more highly and broadly expressed when RNAi is attenuated by inactivation of the Argonaute gene rde-1 (Supplementary Fig. 12)...transgenes are generally expressed at higher levels when RNAi is defective. Quantitative RT–PCR revealed that eri-6/7 mRNA levels are not increased in animals lacking RDE-1 (data not shown)."
Expression Data Expression pattern data (flagged-done): Temporal and spatial (e.g. tissue, subcellular, etc) distribution of genes in a wild-type background. Include: Reporter gene analysis, antibody staining, In situ hybridization, RT_PCR, Western, Northern. Exclude: all markers (antibodies or reporter genes) used to label certain tissues or subcellular structure. This flag also alerts curators for cross-checking CCC semi-automation for missed papers. Further clarification "Figure 2. HCF-1 Is a Ubiquitously Expressed Nuclear Protein"; "eri-7 promoter::gfp and eri-6 promoter::rfp transgenes are expressed in overlapping patterns, with co-expression in hypodermal cells and two pairs of sensory head neurons (ASK and ASI; Fig. 2c). The eri-7 promoter also expresses in the somatic gonad.",
Marker Transgene marker Reporters used to mark certain tissue, subcellular structure or life stage.: Tissue-specific Integrated only transgene and antibodies markers. Reporters used to mark certain tissue, subcellular structure or life stage. Do not flag constructs used as injection markers or any reporter constructs that are not integrated.,
Microarray Microarray(flagged-done): Any microarray data "yes"
in progress RNAi RNAi(flagged-done): Phenotypes/results are discussed for less than 100 RNAi experiments "yes"
Large-Scale RNAi RNAi(flagged-done): Phenotypes/results are discussed for more than 100 RNAi experiments "yes"
DONE Transgene Integrated transgene (flagged-done): Reagent: Textpresso will extract cononical transgene names (e.g. xxIn#). Flag paper if an integrated transgene is discussed but does not have a canoncial name and or if a strain was used that contains an integrated transgene that was not already picked up by textpresso. Patterns; Is, In. Keywords: microbombardment. 'Ex' transgenes are curated when they are used by other experiments, such as phenotype assay or Expr_pattern, so there is no need to flag them. "Textpresso : WBPaper00032232 muIs71 muIs84 rwIs3 xrIs87 -- 20081012 ..."; "table 1"
Overexpression Overexpression (flagged): Over expression of something results in a phenotype "High expression of the constitutively activated SCD-2(neu*) receptor caused 100% of animals to arrest in the first larval stage (L1), with no overt anatomical defects"; "Fig. 6. CRIP overexpression also affects epithelial shape", (add Variation phenotype people)
Structure Information Structural information (flagged): NMR structure, functional domain info for a protein "removal of the first 50aa causes mislocalization of the protein"; "fig.1, fig.8"; "yes, in paper and supplemental materials"; "FIGURE 5. The let-7 sequence is required for formation of the M1 and M2 complexes."; "functional domains of gld-2, fig 3"; "Fig. 3. Comparison of RDE-4 binding properties to variants lacking, or with mutations in, dsRBM1."
Functional Complementation Functional Complementation (flagged): Functional redundancy, rescue by overexpression of extragenic sequence "exc-2 is rescued by exc-9 overexpression"; "...meg-2 functions redundantly with meg-1. Each transgene can rescue the sterility of meg-1(vr10) or meg-1(vr11)... The partial rescue of meg-1 mutants by GFPTMEG-2 suggests that extra copies of MEG-2 can compensate for the absence of MEG-1, implying that the overall level of MEG-1 and MEG-2 is important for proper germline development."; "In transformation experiments, we identified a cosmid, C26G6, which could rescue the egl-32 phenotype. Subclones of this cosmid containing the predicted open reading frame (ORF) T08G11.2 can also rescue egl-32 (Figures 3a & b). Several lines of evidence, however, suggest that egl-32 does not encode T08G11.2, but rather that they are interacting loci"
in vitro Protein Analysis Protein analysis in vitro(flagged): e.g. kinase assay "Fig. 3. Agonist pharmacology of the L-AChR"; "yes"; "fig.1", "Fig. 4. In vitro reconstitution of siRNA production using C. elegans extracts and recombinant RDE-4 variants"
Mosaic Analysis Mosaic analysis (flagged-done): e.g. extra-chromosomal transgene loss in a particular cell lineage abolishes mutant rescue "p.580"; "yes"; "fig2"; "daf-16 mosaic"
Site of Action 'Tissue/Cell. Site of action (flagged-done): e.g. anatomy(tissue/cell)-specific expression rescues mutant phenotype; RNAi in rrf-1 background determines that the gene acts in the germ line "By contrast, a gcy-28.d cDNA rescued chemotaxis when expressed under a panneuronal promoter (Figure 5C), under the AWC-selective odr-3 promoter (Figure 5D), or under the AWCON-selective str-2 promoter (Figure 5E). The results with gcy-28.c suggest that gcy-28 may have roles in multiple neurons; nevertheless, the full rescue with gcy-28.d suggests that gcy-28 can function cell-autonomously in AWCON."; "Whereas mutant smn-1(ok355) animals expressing muscle-directed smn-1 showed only weak phenotypic rescue in a subset of animals, pan-neuronal expression of smn-1 produced stronger rescue effects (Fig. 7A)."
in progress Extract Antibody C. elegans antibodies(flagged-done): New or used antibodies created by labs; skip antibodies bought from companies "in methods";
Covalent Modification Covalent modification (flagged): phosphorylation site is studies via mutagenesis and in vitro assay "Analysis of cDNA sequences derived from the eri-7 pre-mRNA stabilized in rnp-5 RNAi-treated animals revealed adenosine to guanosine transitions at four positions located within the direct repeat (Fig. 2d). These transitions are indicative of adenosine to inosine editing of the eri-7 59-UTR by an adenosine deaminase (ADAR)24"
in progress Extract Allele Newly characterized alleles: No firstpass action. Automated.
Mutant Phenotype for single mutants only Allele(flagged-done): Phenotype is reported for a variation. "Figure 1. hcf-1 Modulates Lifespan...Figure S2. The hcf-1(ok559) Mutant Shows Reduced Brood Size and Increased Embryonic Lethality"; "...smg- 1(r861) null mutants are associated with a fully penetrant protruding vulva phenotype (94%; n= 205)"; "Figure 4 ERI-6/7 is required for endogenous RNAi",,
Non-N2_phenotype : Phenotypes of strains/non-C. elegans
Sequence Change Sequencing mutant alleles (flagged): Mutation was sequenced "the hcf- 1(pk924) mutant has a large deletion that should result in a frame shift leading to an early stop codon, and likely represents a null mutant (Figure S1) [35]."; "table 2: unnamed mutations"; "FIGURE 5. Predicted structure of the glo-3 gene and encoded protein. (A) The structure of the glo-3 gene and the location and phenotypic class of mutations are shown"; "lin-15 mutation p.834"
Gene Interaction and Epistasis Genetic interactions (flagged-done): analysis of more than one gene at a time, e.g. double, triple, etc. mutants, RNAi concurrent with other RNAi-treated worms or mutants "e.g. daf-16(mu86) suppresses daf-2(e1370), daf-16(RNAi) suppresses daf-2(RNAi)"; "hcf-1, daf-16;daf-18, smg-1"; "eri-6, eri-7"; "gene interactions large-scale, table"; "Epistasis analysis in figure 2 and table 2"
Gene Product Interaction Gene product interactions (flagged-done): protein-protein, RNA-protein, DNA-protein interactions, Y2H, etc., "Table S4. PDZ domain specificity prediction"; "Figure 5. Loss of hcf-1 Promotes the DAF-16 transcriptional Regulation of Several Target Genes...Figure 6. HCF-1 Forms a Protein Complex with DAF-16 in C. elegans..."; "Interestingly, the eri-6/7 transsplicing reporter is more highly and broadly expressed when RNAi is attenuated by inactivation of the Argonaute gene rde-1 (Supplementary Fig. 12), suggesting that the eri-6/7 is a target of RNAi..."; "Fig. 1. Identification of genes that regulate clec-85::gfp expression"
Sanger Gene Structure Correction Gene structure correction - need to make sure Sanger is responsible for the clone (flagged): Gene Structure Correction (Gene Structure is different from the one in Wormbase: e.g. different splice-site, SL1 instead of SL2, etc.) "...JA:F59F5.2 targets two predicted genes, F59F5.2 and F59F5.8. Two previously isolated cDNAs, yk1328a05 and yk571h2, suggested that F59F5.2 and F59F5.8 are a single gene that is alternatively spliced to produce two transcripts. We independently isolated F59F5.2/.8 cDNAs from both adult and embryonic stages, supporting the conclusion that F59F5.2 and F59F5.8 are a single gene (see MATERIALS AND METHODS). We refer to the long F59F5.2/.8 transcript as glo-3 and the F59F5.2 transcript as glo-3 short (Figure 5A)."
St. Louis Gene Structure Correction Gene structure correction - need to make sure StLouis is responsible for the clone (flagged): Gene Structure Correction (Gene Structure is different from the one in Wormbase: e.g. different splice-site, SL1 instead of SL2, etc.) "C41D11.1 and C41D11.7 fig.1"; "We confirmed two of three forms by isolation of cDNAs (gcy-28.a and gcy-28.c, corresponding to T01A4.1a and T01A4.1c, respectively) and identified a fourth splice form, T01A4.1d (gcy-28.d), which fuses the upstream predicted gene T01A4.2 to T01A4.1 (Figure 4A)."; "page 3: By contrast, 235 of the indels occurred in regions with no perfectly aligning Solexa read, suggesting a possible error in the C. elegans reference genome,"
Sequence Features Sequence feature (flagged): DNA/RNA elements required for gene expression: promoters, introns, UTR's etc.; DNA binding sites, SL1 SL2 leader sequences "Figure 5. Notch/glp-1 3 UTR elements repress reporter mRNA translation in arrested female gonads."; "Deletion analysis of the lag-2 promoter during dauer indicated that a small fragment located 1.3 kb upstream of the lag-2 translational start site was sufficient for dauer-specific expression in IL2 neurons (Fig. 2A)... We refer to these different classes of binding sites as A and B (Fig. 2B).",
Mass Spec Mass spectrometry (flagged-done): key words: LCMS, COSY, mass spec, HRMS,
Cell/Anatomy Function Cell function (flagged-done): Function of any anatomical part (e.g. cell) is mentioned that has not been flagged already for mosaic analysis, site of action, or ablation data "Figure 3 and Supp table 2 have information on predicted navigation circuit."
Ablation Data Ablation data (flagged-done): cell or anatomical unit was ablated using a laser or by other means (e.g. by expressing a cell-toxic protein) "Killing AWCON in wild-type animals abolished the net migration toward butanone (Figure 3A; Wes and Bargmann, 2001"
Extract New SNP New SNPs (flagged): Reagent: new SNP not already in WB "page 3: By contrast, 235 of the indels occurred in regions with no perfectly aligning Solexa read, suggesting a possible error in the C. elegans reference genome,",
retired? Extract SNP Verified by St. Louis (flagged): Authors report reference genome is incorrect "fig.2: two SNPs mentioned"; any SNP mentioned; "For nekl-1, cDNA clones indicated that the predicted gene annotation was incorrect.",
Supplemental Material Supplemental materials (flagged-done): Flag if supplemental material was not already downloaded. yes
in progress Chemicals Chemicals (flagged): used in assays, what about mutagens? paraquat;butanone, benzaldehyde; aldicarb
in progress Human Diseases Human disease (flagged): Genes discussed are homolog/ortholog of a human disease gene "The INhibitor of Growth (ING) family of type II tumor suppressors are encoded by five genes in mammals and three genes in C. elegans...Here we identify and characterize ing-3, the C. elegans gene with the highest sequence identity to the human ING3 gene."; "Deletion of smn-1, the Caenorhabditis elegans orthologue of the spinal muscular atrophy gene, results in locomotor dysfunction and reduced lifespan"; "alpha-synuclein"; "In this paper, we report on the identification of a HAP1 Caenorhabditis elegans homolog called T27A3.1. T27A3.1 shows conservation with rat and human HAP1, as well as with Milton, a Drosophila HAP1 homolog."; "VAP proteins (human VAPB/ALS8, Drosophila VAP33, and C. elegans VPR-1) are homologous proteins with an amino-terminal major sperm protein (MSP)... A point mutation (P56S) in the MSP domain of human VAPB is associated with Amyotrophic lateral sclerosis (ALS)"
Comment (flagged): e.g. no curatable;review;the paper is used for functional annotations stays in Postgres