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home 1d 2d 3d 1d 3d 1d 3d 3d 3w 6w ORF DNA Tag MS LmxM.01 LmxM.02 LeishGEM.org Data Browser Getting started * Each row in the list represents data from a gene. * Filter the genes using the search box at the top. * To view details about a single gene, click on a row. List entries Each line in the list represents a gene in the Leishmania mexicana genome. The colours concisely represent the LeishGEM results for a particular gene. This is illustrated in the following example: -------------------------------------------------------------------------------- 24h48h72h24h72h24h72h3d3w6wORFDNATagMSPromastigotegrowtharrow_downwardAmastigotegrowtharrow_downwardMacrophageinfectionarrow_downwardMouse footpadinfectionarrow_downwardGenotypingarrow_downwardLocalisationarrow_downward Colour scheme No data available yetPositive / data availableNegative / not includedNot survived / failed- Fitness +-log(p) -------------------------------------------------------------------------------- In the per-time point assay results, a dark gray entry means that no data is available yet. This could mean that this cell line has not been generated yet, or that DNA from the particular assay has not yet been sequenced. In most cases, this data will appear as the project progresses, however for some genes cell line generation might prove impossible. A light gray entry indicates that no significant phenotype has been detected in this time point of this particular assay. Red or blue shading indicates a deleterious or beneficial fitness phenotype was detected, respectively. The colour intensity indicates the strength of the detected fitness phenotype. -------------------------------------------------------------------------------- In the genotyping ORF column, a positive (turquoise) entry indicates that the gene's open reading frame (ORF) could not be detected using PCR and that the generation of the knockout cell line was likely successful. A magenta entry means the ORF was detected. Likewise, a positive entry in the DNA column indicates that genomic DNA was detected after cell line generation. A yellow entry in both the ORF and DNA columns means that the cell line has not survived; another transfection attempt might be forthcoming in the future. -------------------------------------------------------------------------------- A positive entry in the LeishTag localisation column indicates that a tagged cell line was successfully generated and a localisation was found from the resulting microscopy images. A negative entry means that this gene was not scheduled to be tagged and imaged in the LeishTag sub project. A positive entry in the mass spectrometry (MS) column indicates that the protein resulting from the gene has been detected and a localisation was found using LOPIT. A grey entry means that the protein was detected but no localisation could be assigned. If the protein was not detected in the MS run, a negative entry is displayed. Example In the ficticious example knockout cell line above, the information given is: * There is no data yet for the promastigote growth assay. * In the axenic amastigote assay, the cell line showed a mildly detrimental phenotype in the early time point which becomes extremely strong in the late (72h) time point. * In the in vitro macriphage infection assay, no statistically significant phenotype could be detected. * In the in vivo mouse footpad infection assay, no statistically significant phenotype was detected in the early time point, however a mildly beneficial phenotype developed in the middle time (3w) point which became extremely beneficial in the late (6w) time point. * Genotyping confirmed that the open reading frame (ORF) could not be detected in PCR, and that genomic DNA was successfully extracted after cell line generation. * The gene is not scheduled to be tagged and imaged in the LeishTag project, but it was successfully localised in a cell compartment using mass spectroscopy / LOPIT. arrow_upwardarrow_downward Please enable JavaScript to continue using this application. TERMS FOR DATA USAGE The LeishGEM data browser provides access to deletion mutant fitness phenotype and the subcellular localisation of all proteins encoded in the Leishmania genome. This data is being made available to the community as it is generated. Until the project is complete, data usage terms are based on the Fort Lauderdale agreement, an agreement reached for pre-publication usage of genome data. Data on browse.Leishgem.org is available immediately and free to use with acknowledgement. However until the project is complete: * You must contact us before scientific publication or commercial application of research informed by this data. Please email: Richard Wheeler * One of the LeishGEM team will work with you to share our raw data on the proteins of interest, help with advanced searches for cohorts or patterns, etc. * For publications concerning one or two genes we will typically request acknowledgement and citation of this website as a data resource. * For publications concerning more than two genes we reserve the right to have members of the LeishTag team as co-authors, with the rights this entails. This will typically be the one person you collaborate with but, for example for extremely large cohorts of genes, may include others. * Commercial applications will be considered on an individual basis. To use this resource you must agree to these terms. This website uses of cookies to track your preferences and website usage statistics. Accept