WormMine: ExpressionCluster WBPaper00026952:class_D

• Algorithm: Raw data from each experiment were downloaded from the Stanford Microarray Database into Excel files and processed as follows: (i) sort by Spot Flag and discard any rows where the Spot Flag value was nonzero, indicating a bad PCR; (ii) sort by Failed and discard any rows where the Failed value was nonzero, indicating abnormal hybridization; (iii) import into a common file for each type of experiment (i.e., lin-14 or lin-4) the columns from each raw experimental file [RAT2(R/G), which shows a log base 2 transformed ratio of normalized red/green signal for each spot; name of spot (Wormbase designation); chromosome location and description (www.wormbase.org)]; (iv) calculate an average RAT2(R/G) based on the 2 or 3 values (avg; any rows which had only one good experimental value were discarded); (v) calculate a standard deviation (stdev) for the average value; (vi) calculate a t value for each spot by using the formula t = avg*[sqrt(n - 1)]/stdev, where n is the number of experiments for which good data exist, sqrt is square root, and stdev is standard deviation; (vii) sort by absolute t value and discard any rows with a t value below 4.303 (below 95% confidence interval for three experiments) or below 12.706 (below 95% confidence interval for two experiments); (viii) sort by absolute average value and discard any rows with average values below 1.0 (less than twofold change compared to control).
• Description: Class D gene expression showed up regulation in lin-14(lf) in L1, down regulation in lin-4(lf) in L2.
• Primary Identifier: WBPaper00026952:class_D

0 Anatomy Terms

5 Genes

WormBase Gene ID	Gene Name	Sequence Name	Organism
WBGene00000895	dac-1	B0412.1	Caenorhabditis elegans
WBGene00002116	ins-33	W09C5.4	Caenorhabditis elegans
WBGene00009706	argk-1	F44G3.2	Caenorhabditis elegans
WBGene00010253	F58E6.4	F58E6.4	Caenorhabditis elegans
WBGene00011676	cyp-13A2	T10B9.7	Caenorhabditis elegans

0 Life Stages

0 Processes

2 Regulated By Gene

WormBase Gene ID	Gene Name	Sequence Name	Organism
WBGene00002993	lin-4	F59G1.6	Caenorhabditis elegans
WBGene00003003	lin-14	T25C12.1	Caenorhabditis elegans

0 Regulated By Molecule