It is possible to set up two types of relationships between loci when creating a CPG Map: Homology group and ownership relationships. These two types of relationships impose different highlighting rules when a locus is highlighted. Both are very generic and don't specifically represent particular genetic relationships as they could be applied to various different types.
 | Homology Group |
This is the more useful and describes the comparative mapping relationships between maps but it can also describe relationships within maps. The result of this relationship is that when a user highlights a locus, it is highlighted in red as are all other loci in that homology group. These other loci can be in the same double/single map or on neighboring ones.
You can think of the homology group relationship as having a number of buckets each with a number of loci names in it. When a locus is highlighted, the program goes away and looks in all the different buckets. If it finds the locus name in a bucket, it sees who else is in the same bucket and colours them in in red along with the clicked locus. In this respect it is a multi-way/equivalency relationship; clicking on any locus in a homology group highlights the whole lot.
To set up homology group relationships, an identical string should be fed in to the Homology Group variable in the CPG_Locus objects that you want to be in the same group. This string is analogous to the name of the bucket. For example, you could use the string "Bucket numero uno". Or if you had a probe called xp109 that mapped to a number of species, you might fill in "xp109" in the Homology Group variable of each CPG_Locus it mapped to. In fact you can enter any string as long as it is not equal to the zero character or null, i.e. you could actually use "Bucket numero uno" to describe the xp109 homology group! You just have to have a unique name for each homology group.
The program goes away and makes a vector-table of homology groups to use as a reference. The internal representation can be illustrated by the following table:
Vector Entry 0 1 2 3 ... n Homology Group name (=bucket) Group1 Any old sTring will do Bucket nUmErO 11010 the enD Members Map Number Map Number Map Number Map Number Map Number Map Number 0 17 1 99 5 45 1 34 1 78 2 5 2 34 3 25 3 64 2 56 3 25 10 98 2 78 4 3 6 7 0 21
| Ownership |
Ownership relationships are a fair bit different. For a start they can only be set up within a double or single map- not between maps. The word 'ownership' is perhaps a little misleading but describes a hierarchical relationship whereby certain loci have higher level relationship. An analogy can be derived from the following 'tree' structure with lots of nodes.
In this diagram a node 'owns' another if it is connected downstream (to the right of it) by a line to another node. So node 10 owns 15, 16 and 17. As 15 owns 18, 10 also owns 18. Node 18 does not own anyone! Node 1 owns every node in this case.
In CPG Map, if you click on a locus ( == node) it gets highlighted in red. Any other loci that it owns are then highlighted in orange. This is a one-way relationship as if you click on one of the orange loci, it does not highlight the loci it is owned by, only if an ownership relationship has been set up the other way.
Although a generic relationship, it would be useful for describing biological cascade type relationships such is found in signal transduction pathways or transcription factors. For example, if you were to click on a locus corresponding to a transcription factor, the loci that it controls would be highlighted in orange. Clicking on one of those loci would not cause any others to highlight unless an ownership relationship was set up the other way.
To set up the ownership for a CPG_Locus, an integer array containing a list of numbers corresponding to the entries in the vector of the other loci that the locus owns is passed to it.
Please note:
| In the diagram above if you clicked on locus 1, loci 2 and 3 would be highlighted in orange, that's all, i.e. not all the loci even though locus 1 owns them all. If you click locus 3, 9 and 8 get highlighted. I was originally going to create a colour cascade whereby if you clicked on locus 1, 2 and 3 would be painted orange, the ones below them green, the ones below them pink or some other colour. I thought this might look visually confusing! It's certainly confusing enough describing it! |
| A locus can be owned by multiple parent loci. So if a gene is used in two different cascade pathways, it could be set up to have two parents. |
| Ownership can be set up to be two-way if you want- you would have to set up the relationship going the other way as well. |
