Basic HTML Version
Leukemic T-cell Precursors from T-lineage All Patients Characterized by Profound Ku80 Deficiency
9
Figure 5 Expression levels of
Ku
,
Ikaros
, and
Ikaros
target genes in Normal vs. Leukemic Bone Marrow Cells
Note: We compiled the archived “Microarray in Leukemia (MILE)” gene expression profiling data on primary leukemic cells from
174 T-lineage ALL patients and 74 normal bone marrow specimens (GSE 13159). We compared 74 normal bone marrow specimens
vs, 174 leukemic (T-lineage ALL) bone marrow specimens for expression levels of 26 IK target genes represented by 40 transcripts
on the Affymetrix human genechips, 3
IKZF1
transcripts, 2
Ku80
(
XRCC5
) transcripts and 1
Ku70
(
XRCC6
) transcript. Transcript
signal values obtained from hybridization onto the Affymetrix Human Genome U133 Plus 2.0 Arrays were calculated using
non-central trimmed mean of differences between perfect match and mismatch intensities with quantile normalization (DQN3).
Differential were compared using T-tests utilizing the DQN3 values (2-sample, Unequal variance correction, p-values<0.05 deemed
significant). Gene expression values were transformed into standard deviation units calculated from the mean and standard deviation
expression values for all the samples in each study and effect sizes were reported using differences standard deviation units between
comparison groups. We used a one-way agglomerative hierarchical clustering technique to organize expression patterns using the
average distance linkage method such that genes (rows) having similar expression across samples were grouped together (average
distance metric). Dendrograms were drawn to illustrate similar gene-expression profiles from joining pairs of closely related gene
expression profiles, whereby genes joined by short branch lengths showed most similarity in expression profile across samples. The
heat map depicts genes up regulated expression values in red and down regulated expression values in green. (C) Expression of 2
probesets for
XRCC5
/
Ku80
(208642_s_at and 208643_s_at) were compared between 74 normal bone marrow specimens and 174
Molecular Medical Science, Int’l Journal of