Nielder at 19:35, 9 February 2016

2016-02-09T19:35:36Z

Nielder: Created page with "Nick Elder Group 2 intestines"

2016-02-09T18:39:26Z

Created page with "Nick Elder Group 2 intestines"

New page

[[Nick Elder]]

[[Group 2 intestines]]

← Older revision		Revision as of 19:35, 9 February 2016
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		+	Clustering:
		+	*Grouping genes, samples, etc.
		+	**may present the order in a way that does not reflect how would would expect/want it to
		+	*Can be used to pull out patterns and make predictions
		+	*Induction can look much more dramatic than repression
		+	*Changing the y-axis to a logarithmic scale reveals much more drastic changes in repression
		+	**Similar relationships could be caused by direct interaction or co-regulation
		+	**Strong negative correlation could be as interesting as positive correlation
		+	***Computers are more likely to group positive correlations
		+	*Gene Expression Profiles (Guilt by Association)
		+	**comparing genes or expression levels in samples over time
		+	**Correlation, Euclidean distance, Hamming Distance, etc....
		+	**Correlation is very sensitive to outliers; also, very small changes, possibly due to noise, can be interpreted as correlation with more drastic changes
		+	*Linkage Methods
		+	**Can take the nucleus/average of a cluster and compare that to a desired single gene
		+	**Can average all the distances between all points
		+	**Can compare the gene of interest to all the rest of the genes individually
		+
		+	*Hierarchical clustering
		+	**Joins two most similar genes
		+	**Join next two most similar "objects" (genes or clusters of genes)
		+	**Repeat until all genes have been joined
		+	**Once clustered, two genes can, under no circumstances, under penalty of death, in no way possible on heaven or earth, be split apart
		+	**No gene left behind. Everyone has to be in the cluster; starts at +1 correlation and end at -1 correlation
		+	***Genes that are most distant in the cluster (opposite correlation) could be co-regulated together
		+	**Cutting the tree
		+	***Draw a line to separate the clusters
		+	****Decision to cut the line is completely arbitrary
		+	*K-means Clustering
		+	**Specify how many clusters to form - just break into groups, not breaking the tree
		+	**Randomly assign each gene to one of K different clusters
		+	**Average expression of all genes in each cluster to create K pseudo genes
		+	**Rearrange genes by assigning each other to the cluster represented by the pseudo gene to which it is most similar
		+	**Repeat until convergence
		+	*Supervised Clustering
		+	**Find genes in expression file whose patterns are highly similar to a desired gene or pattern
		+	**Add closest gene first
		+	**Then add gene that is closest to all genes already in cluster
		+	**Repeat, as long as added gene is within specified distance to genes already in the cluster
		+	**Distance from one gene to a set of genes defined to be maximum (or minimum or average) of all distances to individual members of the set (complete, single, and average linkage, respectively)
		+	**Dr. C says that it might be really nice to cluster genes that move with a transcription factor, since a little induction in the transcription factor can have major effects on other gene expression
		+	*Quality Clustering: QT Clust
		+	**Each gene builds a supervised cluster
		+	**Gene with "best" list, and genes in its list, becomes the next cluster
		+	**Remove these genes from consideration, and repeat
		+	**Stop when all genes are clustered, or largest cluster is smaller than user specified threshold
		+	**Make 'cliques', find the largest, separate that group, remove all members from that group from all other groups, and make the next largest group from the existing members.

NHE Feb 9 Notes - Revision history

Nielder at 19:35, 9 February 2016

Nielder: Created page with "Nick Elder Group 2 intestines"