When enabled, cluster data appears as blue circles or squares drawn as overlays on the pseudoarray image. These options are discussed in the section on clustering.
Cluster analysis plots include finding a subset of genes or subsets of samples based on cluster analysis of expression profile similarity measures. These show genes belonging to particular clusters, or genes that cluster well with specified genes. Cluster methods include: finding genes similar to the current selected gene within a "distance" threshold; K-means-like clustering where you specify a seed gene and the number of clusters; and hierarchical clustering with clustergram and dendrogram graphics.
Figure 2.4.5 Cluster Menu options. The hierarchical clustering option is being selected.
There are many methods for doing clustering - each with advantages and disadvantages. We present three methods in MAExplorer and plan on adding a variety of more powerful methods through the MAEPlugin facility under development.
These methods may find genes belonging to particular clusters or genes that cluster well with particular genes. Gene clusters are sets of genes whose expression profiles are found to be similar according to a particular metric. We now define what we mean by "similar". The order list of hybridized samples used in computing the expression profiles are those in the HP-E list. MAExplorer has two different dissimilarity measures for Cij: Euclidean distance LSQdistij and Pearson correlation coefficient rij. These are computed as follows and are tested against the cluster distance threshold (set by the slider in the preferences sliders). Let n= |HP-E|, the number of samples in the expression profile. We define similarity as (1.0 - normalized dissimilarity).
| Hint: when working with very large data sets with many samples, it may be useful to pre-adjust the distance and/or number of clusters threshold sliders to an approximate range using the (Edit Menu | Preferences | Adjust all Filter threshold scrollers). This is because once the clustering starts, it does not (currently) let you abort the clustering to change the threshold value. |
LSQdistij = Sqrt( Sum ( D'hj - D'hi) **2 ) / n
h in HP-E
i,j in Filtered genes, i not j
Let,
sumij = Sum( D'hj * D'hi ),
mni = (1/n)Sum( D'hi ),
mnj = (1/n)Sum( D'hj ),
sumSqi = Sum( D'hi * D'hi ),
sumSqj = Sum( D'hj * D'hj ),
then,
[sumij - n*(mni * mnj)]
rij = --------------------------------------------------------
[Sqrt(sumSqi - n*n*mni*mni) * Sqrt(sumSqj - n*n*mnj*mnj)]
h in HP-E
i,j in Filtered genes, i not j
The Cluster plots submenu contains a number of clustering methods. Pressing the Escape key during a long cluster operation will abort the operation. If you are in stand-alone mode using the ClusterGram, a SaveAs GIF button will also be available for saving the current plot as a full resolution GIF file specified by the user in a popup file browser window.:
Cluster genes with
expression profiles similar to current gene [RB] - click on
gene in image to find other genes with similar HP-E expression
profiles whose cluster distance is less than the cluster
distance threshold. The larger the blue
box, the higher the similarity.
Cluster counts of
similar Filtered genes by expression profiles [RB] - draw
blue circles around filtered genes
indicating the number of other genes whose cluster similarity is
less than the cluster distance threshold. The larger the circle,
the more similar genes were found. Clicking on a gene switches
to the above mode.
K-means clustering of
gene expression profiles [RB] - draw
magenta circles around the N primary-node gene clusters
representing the gene closest to representing the center of the
cluster. Each of the nodes is a maximum distance from all other
nodes in the recursive definition of nodes. N is determined by
the State Scroller "# of Clusters". Changing N will recompute
the clusters. It then pops up a scrollable text window with the
clusters and indicates which genes belong to it. If you select
the EP plot button, it will draw the expression profiles
for the clustered genes. The Mn-Cluster-Report button
will generate report for all genes sorted by K-means
cluster. Summaries can be generated using the Mean EP
plot and Mn-Cluster-Report buttons. The SaveAs
GeneSets button saves all of the clusters as named Gene Sets
("Cluster #1", "Cluster #2", etc). If you change the filter or
current gene, you should explicitly use the Recompute
Clusters button to regenerate the new set of clustered
genes. When you recompute the K-means clusters, it uses the
current gene as the initial node.
- this computes the hierarchical
clustering of the expression profiles (normalized by HP-X sample
data for each gene) of Filtered genes. The hierarchical
clusters are displayed in an ordered gene clustergram and
optional dendrogram. Sub-regions of the clustergram may be
explored in more detail using the EP-subset plot button,
or a report of the ordered genes can be created using the
ClustGram Report Note: you may add (remove) genes you
select from the Clustergram to the E.G.L. by holding the
Control(Shift) key while clicking on the gene name.
S.O.M. gene clusters by
expr profiles [RB] - [Future MAEPlugin]
Multi-Dimensional
Scaling of genes by expr profiles [RB] - [Future MAEPlugin]
Multi-Dimensional
Scaling of genes by exprprofiles [RB] - [Future MAEPlugin]
Clusters of (HP-E)
samples as fct of Filtered genes [RB] - [Future]
Use correlation-coefficient
else Euclidian-distance [CB] - use the (1.0 - correlation
coefficient) as the distance metric instead of the default
Euclidean distance.
Scale EP vector by max
magnitude prior to clustering [CB] - scale each sample in
the EP by the max magnitude for all sample values in the EP.
Normalize by HP-X sample else
HP max intensities [CB] - normalize data by the
corresponding HP-X sample data for each gene or the maximum raw
intensity for each HP in the expression profile.
Use median instead of mean
for K-means clustering [CB] - use the clustering (see (Bickel, 2001)).
The Hierarchical Cluster plots submenu contains:
Display ClusterGram of gene
expr profiles [CB] - compute the hierarchical clustering of
the expression profiles (normalized by HP-X sample data for each
gene) of Filtered genes. Then display the hierarchical clusters
in an ordered gene clustergram and optional dendrogram when the
dendrogram checkbox is selected. Expression profile
plots of the clustergram may be explored in more detail using
the EP plot button that generates a scrollable list of
all EP plots ordered by the same order as the clustergram. A
full report of the ordered genes expression profiles may be
created using the ClustGram Report button.
Use avg-arithmetic-linkage [RB] - set the hierarchical
clustering linkage method to the average arithmetic linkage of
sub-clusters.[ Future]
Use avg-centroid-linkage
[RB] - set the hierarchical clustering linkage method to
average centroid linkage of sub-clusters (default).
Use next-min-linkage
[RB] - set the hierarchical clustering linkage method to the
next minimum distance sub-cluster linkage in random order.
Use cluster-distance matrix
cache [CB] - if you do not have enough memory for clustering
large gene sets, disable the cache. It will take MUCH longer
without the cache. When clustering, if there is
not enough memory available for the cache, it will warn you and
suggest you either reduce the number of genes being clustered or
use a computer with more memory.)
Use short else float
cluster-distance matrix cache [CB] - if there is not enough
memory for the set of genes you wish to cluster and you still
want to use the cache, you can use 16-bit (i.e. short) data
instead of the 32-bit (i.e. float) data. The results will be
less precise.
Use un-weighted else
weighted average [CB] - set the hierarchical clustering vector
averaging to un-weighted (the default weights it by the number
of genes in that sub-cluster). Otherwise using weighted gives
equal (0.50) weighting to each sub-cluster.
Figure 2.4.5.1 Similar genes clustered to the current gene. This method finds all genes that are similar to the current gene as those defined by their distance between expression profiles being less than the threshold set by the user. Each gene that passes the cluster distance threshold test is indicated in the image with a blue square where the size of the square is proportional to its similarity. This data is from the 38 samples in the MGAP database containing duplicated spots. A) Main windows with popup cluster similarity report and cluster distance threshold slider. B) Scrollable list of EPplots of similar genes with the red error bars indicating the variation for duplicated spots for each HP sample. The Err checkbox may turn the error bar overlays on and off.
For both of these commands, if you want to view the expression profile plots, click on the EP plot button in the cluster window and it pops up the scrollable expression profiles window. If you click on a gene in the image, it will select it as the new current gene and seed gene and recompute the cluster of genes most similar to the new see gene.
For both of these commands, if you want a permanent report, click on the "Cluster Report" button in the cluster window and it will generate a report in the current modality (i.e. scrollable spreadsheet or tab-delimited). You may switch between these two modes by pressing the "Go '...'" button in the report.
Figure 2.4.5.2 Display of cluster counts for all genes less than the cluster threshold from MGAP 38 sample database. The algorithm counts the number of similar genes for each Filtered gene and draws a blue circle whose size is proportional to the number of genes similar to that gene. That is why there are a larger number of the larger circles.
Figure 2.4.5.3 Genes clustered using the K-means cluster method. A) Using the current gene as the initial cluster, MAExplorer finds N orthogonal clusters assigning the set of filtered genes to these clusters using the HP-E expression profiles. All genes are iteratively assigned to these clusters. Genes belonging to the current cluster are labeled with a green cluster number both in the array and in the scatter plot. The slider determines the number of clusters (set to 6 here). A 2D scatter plot shows the genes belonging to cluster 6. The K-means cluster report on the right contains a sorted list of the genes in each cluster and has buttons to generate EP plots and reports as well as summary mean EP plots (shown) and mean cluster reports. The detailed list is shown below. B) Part of the scrollable EP plots for this data showing genes belonging to both clusters #5 and #6. C) The mean EP plots for the 6 clusters.
Cluster report for 6 K-means clusters with 141 genes being clustered. The seed gene is [1248564] Jun-B oncogene. Clone ID Similarity Cluster-# Distance-to-cluster Gene-Name -------- -------------- --------- ------------------- ---------------- 1248411 ************** 1 Cluster [26 genes] in cluster [distNext: 1.035] wiCdist:mn+-sd=1.223+-0.453 CV=0.371 Calpactin I light chain 1381592 ********** 1 0.448 Surfeit gene 4 1247956 ********* 1 0.706 Protein kinase, cAMP dependent, catalytic, beta 1381836 ******** 1 0.761 Prohibitin 1382325 ******** 1 0.771 M.musculus mRNA for C1D protein 1248270 ******** 1 0.775 Seven in absentia 1A 1247716 ******** 1 0.794 Lipoprotein lipase 1248184 ******** 1 0.847 Mus musculus bromodomain-containing protein BP75 mRNA, complete cds 1248564 ******* 1 0.864 Jun-B oncogene 1382667 ******* 1 0.888 SERINE/THREONINE PROTEIN PHOSPHATASE PP2A-BETA, CATALYTIC SUBUNIT 1382561 ******* 1 0.931 Mus musculus GTP-specific succinyl-CoA synthetase beta subunit (Scs) mRNA, partial cds 1248089 ****** 1 1.013 M.musculus RPS3a gene 1247780 ****** 1 1.088 Proprotein convertase subtilisin/kexin type 7 1247557 ****** 1 1.104 M.musculus L28 mRNA for ribosomal protein L28 1248321 ***** 1 1.278 Decay accelerating factor 1 1382751 **** 1 1.311 Clusterin 1382007 **** 1 1.357 Murine mRNA with homology to yeast L29 ribosomal protein gene 1382074 **** 1 1.390 Orosomucoid 1 1381963 **** 1 1.417 M.musculus mRNA for ribosomal protein L36 1248278 ** 1 1.658 HISTONE H3.3 1247630 ** 1 1.675 Procollagen, type I, alpha 2 1247865 * 1 1.837 Mouse beta-D-galactosidase fusion protein mRNA, complete cds 1382236 * 1 1.85 Caspase 7 1247833 1 1.882 Mus musculus radio-resistance/chemo-resistance/cell cycle checkpoint control protein (Rad9) mRNA, complete cds 1248535 1 1.953 M.musculus mRNA for selenoprotein P 1247702 1 2.157 Cytochrome C oxidase, subunit Va 1382282 ************** 2 Cluster [13 genes] in cluster [distNext: 24.199] wiCdist:mn+-sd=16.184+-6.667 CV=0.412 Max interacting protein 1 1382159 ********** 2 9.086 TRANSPLANTATION ANTIGEN P35B 1247854 ********* 2 11.002 Prolyl 4-hydroxylase, beta polypeptide 1247970 ******** 2 11.786 Mouse mRNA for osteoblast specific factor 2 (OSF-2) 1381663 ******** 2 12.948 Mus musculus vacuolar adenosine triphosphatase subunit A gene, complete cds 1382100 ******** 2 13.34 T-complex protein 1, related sequence 1 1248366 ******** 2 13.541 Mus musculus cytochrome c oxidase subunit VIIa-L precursor (Cox7al) mRNA, nuclear gene encoding mitochondrial protein, complete cds 1247568 ******** 2 13.762 Cathepsin D 1247872 ******* 2 14.015 Mus musculus endothelial monocyte-activating polypeptide I mRNA, complete cds 1382333 ******* 2 14.065 Stromal cell derived factor 5 1382008 ******* 2 15.985 Mus musculus FK-506 binding protein homolog (SAM11) mRNA, complete cds 1247724 **** 2 21.964 Glutathione-S-transferase, alpha 3 1247846 2 34.704 House mouse; Musculus domesticus kidney mRNA for Phosphatidic acid phosphatase, complete cds 1247945 ************** 3 Cluster [22 genes] in cluster [distNext: 11.979] wiCdist:mn+-sd=7.559+-3.347 CV=0.443 Mus musculus mRNA for DEDD protein 1247797 ********** 3 4.159 Mus musculus Btk locus, alpha-D-galactosidase A (Ags), ribosomal protein (L44L), and Bruton's tyrosine kinase (Btk) genes, complete cds 1382087 ********** 3 4.494 Cell division cycle 42 1247539 ********** 3 4.511 EST 1248212 ********** 3 5.009 Murine mRNA for integrin beta subunit 1248470 ********** 3 5.044 EST 1247521 ********* 3 5.299 Mus musculus mRNA for peroxisomal integral membrane protein PMP34 1381808 ********* 3 5.924 Mus musculus UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-T3 mRNA, complete cds 1381970 ********* 3 6.285 Mus musculus thioredoxin mRNA, nuclear gene encoding mitochondrial protein, complete cds 1382168 ********* 3 6.343 N-terminal Asn amidase 1382704 ********* 3 6.36 Mus musculus N-myristoyltransferase 1 mRNA, complete cds 1248548 ********* 3 6.378 Mus musculus WDR protein mRNA, complete cds 1247564 ******** 3 6.652 Erythrocyte protein band 7.2 1248588 ******** 3 6.67 M.musculus BAP31 mRNA 1247541 ******** 3 6.690 Apolipoprotein D 1248462 ******** 3 7.322 Sterol O-acyltransferase 1 1248462 ******** 3 7.42 Sterol O-acyltransferase 1 1248521 ****** 3 9.121 Mus domesticus nuclear binding factor NF2d9 mRNA, complete cds 1382212 ****** 3 10.137 Thyroid autoantigen 70 kDa 1382270 ***** 3 10.529 Voltage-dependent anion channel 2 1248152 ***** 3 10.541 M. musculus mRNA for MAP kinase-activated protein kinase 2 1247678 3 19.431 Casein alpha 1247543 ************** 4 Cluster [44 genes] in cluster [distNext: 1.035] wiCdist:mn+-sd=0.439+-0.266 CV=0.606 RAS-related C3 botulinum substrate 1 1381923 ************ 4 0.158 Prolyl 4-hydroxylase, beta polypeptide 1382052 ************ 4 0.209 Trans-acting transcription factor 1 1247882 *********** 4 0.237 Mus musculus AMP activated protein kinase mRNA, complete cds 1248099 *********** 4 0.246 Mus musculus mitogen-responsive 96 kDa phosphoprotein p96 mRNA, alternatively spliced p67 mRNA, and alternatively spliced p93 mRNA, complete cds 1248351 *********** 4 0.251 Abl-interactor 1 1247540 *********** 4 0.255 Mus musculus mRNA for ZIP-kinase, complete cds 1248316 *********** 4 0.26 Mus musculus proteasome alpha7/C8 subunit mRNA, complete cds 1382671 *********** 4 0.264 Mouse MA-3 (apoptosis-related gene) mRNA, complete cds 1382014 *********** 4 0.277 Transcription elongation factor B (SIII), polypeptide 1 (15 kDa),-like 1247885 *********** 4 0.289 Mus musculus mRNA for ryudocan core protein, complete cds 1248294 *********** 4 0.292 Mus musculus thioredoxin-related protein mRNA, complete cds 1382066 *********** 4 0.306 Inhibitor of DNA binding 2 1248597 *********** 4 0.307 Lipocortin 1 1248591 *********** 4 0.324 Interferon beta, fibroblast 1248445 ********** 4 0.333 Mus musculus beta prime coatomer protein mRNA, partial cds 1247775 ********** 4 0.34 House mouse; Musculus domesticus male brain mRNA for ARF1, complete cds 1382750 ********** 4 0.340 Thymoma viral proto-oncogene 1247905 ********** 4 0.341 Monokine induced by gamma interferon 1381668 ********** 4 0.351 Mus musculus mitogen-activated protein kinase-activated protein kinase mRNA, complete cds 1381811 ********** 4 0.356 Protein tyrosine phosphatase, receptor type, D 1382031 ********** 4 0.358 Protease (prosome, macropain) 28 subunit, beta 1248345 ********** 4 0.363 Mus musculus alpha-methylacyl-CoA racemase mRNA, complete cds 1382555 ********** 4 0.364 Lysosomal membrane glycoprotein 1 1247820 ********** 4 0.367 Tight junction protein 1 1247598 ********** 4 0.374 Retinoblastoma 1 1247595 ********** 4 0.378 PROBABLE CALCIUM-BINDING PROTEIN PMP41 1381928 ********** 4 0.379 Mus musculus MRJ (Mrj) mRNA, complete cds 1248196 ********** 4 0.399 Max protein 1381691 ********** 4 0.423 SRY-box containing gene 17 1248225 ********** 4 0.434 Mus musculus heat shock transcription factor 1 (Hsf1) gene, partial cds 1248084 ********** 4 0.442 Mus musculus Supl15h gene 1247941 ********* 4 0.453 Fibroblast growth factor inducible 14 1381623 ********* 4 0.468 Stearoyl-coenzyme A desaturase 1 1248202 ********* 4 0.473 Mouse mRNA for PAP-1, complete cds 1382115 ********* 4 0.512 GLUTATHIONE S-TRANSFERASE GT8.7 1382044 ********* 4 0.515 Cartilage derived retinoic acid sensitive protein 1381636 ******** 4 0.567 Lymphotoxin B 1381920 ******** 4 0.569 Mus musculus mRNA for NEFA protein, complete cds 1247757 ******** 4 0.596 Granzyme B 1382094 ******** 4 0.609 High mobility group protein 1 1247545 ******** 4 0.638 Carbon catabolite repression 4 homolog (S. cerevisiae) 1247607 *** 4 1.188 POLYADENYLATE-BINDING PROTEIN 1247727 4 1.667 Malate dehydrogenase, mitochondrial 1248244 ************** 5 Cluster [19 genes] in cluster [distNext: 3.473] wiCdist:mn+-sd=4.273+-2.059 CV=0.482 CD80 antigen 1248534 ********** 5 1.648 Carbonyl reductase 1247764 ********** 5 1.776 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, GAMMA CHAIN 1381933 ********* 5 2.345 Mouse rpS17 mRNA for ribosomal protein S17, complete cds 1381616 ********* 5 2.42 Mus musculus oral tumor suppressor homolog (Doc-1) mRNA, partial cds 1248232 ********* 5 2.486 Mus musculus putative glycogen storage disease type 1b protein mRNA, complete cds 1382644 ******** 5 2.717 Cyclin G 1248125 ******** 5 2.791 Histocompatibility 2, class II, locus Mb2 1247799 ******** 5 2.869 Mus musculus signal recognition particle receptor beta subunit mRNA, complete cds 1247708 ******** 5 3.024 Ephrin A1 1247932 ****** 5 4.235 Mus musculus (clone: pMAT1) mRNA, complete cds 1382515 ***** 5 4.668 ATPase, Na+/K+ beta 3 polypeptide 1248586 ***** 5 4.838 Mus musculus viral envelope like protein (G7e) gene, complete cds 1248198 *** 5 5.874 Mus musculus D9 splice variant 2 mRNA, complete cds 1381623 ** 5 6.224 Stearoyl-coenzyme A desaturase 1 1382086 * 5 6.885 Mus musculus (strain C57Bl/6) mRNA sequence 1247887 * 5 7.014 Mouse chromosome 6 BAC-284H12 (Research Genetics mouse BAC library) complete sequence 1247886 5 7.810 Cut (Drosophila)-like 1 1248303 5 8.094 Lipopolysaccharide response 1247621 ************** 6 Cluster [17 genes] in cluster [distNext: 19.157] wiCdist:mn+-sd=12.410+-3.024 CV=0.244 Mus musculus Lsc (lsc) oncogene mRNA, complete cds 1248050 ******* 6 7.407 Mus musculus C57BL/6J ribosomal protein S28 mRNA, complete cds 1247698 ******* 6 7.571 Adipocyte protein aP2 1248240 ***** 6 9.198 Mus musculus mRNA, complete cds 1247862 **** 6 9.844 Mus musculus Nmi mRNA, complete cds 1382162 **** 6 10.330 CAMP responsive element modulator 1248398 *** 6 11.007 Mouse mRNA for ribosomal protein S12 1248281 *** 6 11.143 M.musculus mRNA for histone H3.3A 1247852 *** 6 11.576 Twist gene homolog, (Drosophila) 1381991 ** 6 12.809 Prolyl 4-hydroxylase, beta polypeptide 1382753 ** 6 13.019 Mus musculus cleavage and polyadenylation specificity factor (MCPSF) mRNA, complete cds 1248368 * 6 13.639 Mus musculus ribosomal protein S26 (RPS26) mRNA, complete cds 1247639 * 6 13.692 SRY-box containing gene 4 1248435 6 14.262 Thymus cell antigen 1, theta 1247961 6 14.75 ATP SYNTHASE ALPHA CHAIN, MITOCHONDRIAL PRECURSOR 1248344 6 15.217 Gut enriched Kruppel-like factor 1382234 6 16.351 CD8 antigen, beta chain
We call the genes closest to the "center" of the K clusters primary genes and they are reported with additional information. The "Cluster [# genes]" entries in the distance-to-cluster fields indicates that these genes are the center of the clusters (i.e. primary genes). The distNext is the distance from this cluster center to the next nearest K-means cluster center. The number of clusters N (6 in this example) is set in the popup state scroller. If you change the value of N, it will recompute the clusters and the primary genes.
It draws magenta circles around the primary genes in the microarray and the cluster number to the right of the circle. The size of a circle corresponds to the number of genes clustered with that circle. If you click on a gene belonging to any cluster, it defines that cluster as the "current cluster". It will change the labels of the subset of genes that belong to the current gene from red (white) circle to a green (yellow) cluster number of the current cluster in the intensity (ratio) pseudoarray image. In addition, the 'edited gene list' is set to the subset of genes that belong to the current cluster. If you are also displaying a scatter plot, genes in the current cluster have their red '+' characters changed to the cluster number.
Clustering is represented by a binary tree and is visualized as an ordered gene clustergram and optional dendrogram sub-plot. This is similar to the methods of (DeRisi, 1996), (Eisen, 1998), and (White, 1999). Currently, MAExplorer does 1-way clustering - not the 2-way clustering of (Weinstein, 1998) and (Eisen, 1998). Each row of the clustergram represents a gene and each column represents a HP in the HP-E list of samples. Each box in a row represents the normalized expression of that gene for the HP represented in that column. The color of the box is one of 9 colors representing the normalized expression ranges and assigned according to the following table:
Table 2.4.5.4. ClusterGram pseudocolor assignments. The colors are assigned to "box" entries in the clustergram corresponding to genes. The color represents data as either the X/Y ratio or X-Y Zdiff relative to the normalizing HP.
| . | . | . | . | . | . | . | . | . |
| bright green | . | . | dark green | Black | dark red | . | . | bright red |
| <1/8X | 1/6X | 1/4X | 1/2X | 1X | 2X | 4X | 6X | >8X |
Figure 2.4.5.4 Hierarchical clustering clustergram of genes filtered by ratio histogram bins for 19 samples from the MGAP data set. The hybridized samples are drawn as colored boxes in the 19 columns. Rows of boxes correspond to gene expression profiles. In A), the set of all genes and ESTs was filtered by the CV filter set to 0.387 and the normalization was the Zscore. The gene "Mus musculus D9 spice variant 2 mRNA, complete cds" was selected as the current gene in the clustergram. Data for this gene and the selected HP column is indicated at the top of the clustergram. The list of the 19 samples is shown on the left. B) Details of clustergram and dendrogram are shown where the user had selected a cluster distance threshold at "Mouse mRNA for mitochondrial cytochrome c oxidase subunit Vb" in the dendrogram part of the plot (zoomed by 2X). This selection draws all parts of the dendrogram tree that are less than this distance are drawn in red. C) shows the manual selection of genes from the ClusterGram or Dendrogram by clicking on the genes names you wish to capture in the Edited Gene List (EGL) while the Control key is pressed. The zoomed subregion shows three genes in the same cluster that were selected (magenta stars in the right edge of the ClusterGram).
