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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:

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24h48h72h24h72h24h72h3d3w6wORFDNATagMSPromastigotegrowtharrow_downwardAmastigotegrowtharrow_downwardMacrophageinfectionarrow_downwardMouse
footpadinfectionarrow_downwardGenotypingarrow_downwardLocalisationarrow_downward

Colour scheme

No data available yetPositive / data availableNegative / not includedNot
survived / failed- Fitness +-log(p)

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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.

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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.

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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.

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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.

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