Difference between revisions of "UserGuide:Cell Search"
(New page: == Cell Search == One of the much-cited advantages of C. elegans is that its cellular lineage and neuronal wiring are exactly known. WormBase provides several ways to search for specific ...)
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Latest revision as of 18:25, 17 August 2010
One of the much-cited advantages of C. elegans is that its cellular lineage and neuronal wiring are exactly known. WormBase provides several ways to search for specific cells, lineage elements, or neuronal connections. PEDIGREE BROWSER: CELL
Typing a given cell into this window, and then either typing "enter" or clicking on "Show Cell", will cause the specific lineage leading from the fertilized egg (P0) to the cell to be shown below (under 'Full lineage'). One can either search for a cell that has been exactly determined, including which side it is on (e.g., "AWAR") or for cell specified by type but not by laterality (e.g., "AWA"). If one searches for a generic cell, the search will try to interpret this intelligently by showing and highlighting all pertinent cells in their lineages (e.g, lineages to both AWAR and AWAL). See below for details of the 'Full lineage' display.
PEDIGREE BROWSER: LINEAGE
A variety of predefined lineage types are provided for both hermaphrodite and male development. As with a generic cell, all the relevant cells will be shown and highlighted in the 'Full lineage' display.
PEDIGREE BROWSER: CELL GROUP
C. elegans lineages are invariant, or nearly so. The anatomy of the completed animal is also highly invariant. But one does not map onto the other in a simple-minded way: many different components of distinct lineages can coalesce to produce a single organ, tissue, or functional group. WormBase allows users to scan the developmental lineage for the pedigrees of many different predefined cell groups (e.g., "amphid neurons"). Relevant cells are shown and highlighted in 'Full lineage'.
Several different forms of searching cause the 'Full lineage' display to expand into complicated forms. To quickly and cleanly reduce the Full lineage display back to its original, compressed form, one can click on the "Close All" button. This is of most use when one wants to keep the effects of a given search clearly distinct from those of a previous search.
This display begins by showing only the fertilized egg (P0), but expands when a search is done for a given cell, lineage, or group. It can also be expanded by directly browsing (by clicking on a cell marked "+" to get a full display of the cells descended from it).
Cells are given the name most likely to be intelligible to a C. elegans investigator; where a common short name exists for a terminally differentiated cell type (e.g., "SAAVL") that is used, instead of the full-lineage abbreviation (e.g., "ABplpaaaaap"). Where no such short name exists, a full-lineage term is used (e.g., "Earaa").
This display is much like the 'Full lineages' display, except that these lineages are given specifically for postembryonic blast cells that generate ventral cord motoneurons, ventral hypodermis, vulva, and the male preanal ganglion. The lineages begin with blast cells P1 through P12. Due to an oddity in the current implementation, the 'Full lineages' stop with the lineage-names of P1-P9 et al., while the 'Neuronal lineages' start with the short names of P1-P9 et al. This feature may be corrected in future releases of the Wormbase site software.
INDIVIDUAL CELLS (DESCRIBED IN CELL REPORT)
Each individual cell is given a hypertext link; clicking on this link will take one to the appropriate Cell Report. Each such report has the following features: an overview of the cell and its role; what group of cells it belongs to; whether it is terminally differentiated or fated to undergo further division; the ancestry of the cell during development; and the expression patterns of any genes that are known or believed to overlap temporally and spatially with the cell in their activity. Where a given cell type is a neuron, a diagram of its shape in the worm body (excerpted from White et al. , Philos. Trans. R. Soc. Lond. B Biol. Sci. vol. 314, pp. 1-340) is given. Finally, for each cell type, there is a graphical map of the immediate lineage that is given to the right of the text information, and that itself is browsable.