Journal: Cancer Informatics

Article Title: Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map

doi: 10.4137/CIN.S39839

Figure Lengend Snippet: Flowchart of the experimental procedure. Notes: ( A ) Twenty-two samples were analyzed with microarray experiments, and the data were compared with hiPSC 201B7 data from GEO (GSM241846) after normalization. ( b and C ) To detect differentially expressed genes/probes, two parameters were used for gene selection; one is ( b ) |G-A|-2V > 0 and another is ( C ) max–min > average + 2SD. ( b ) G, A, and V are denoted as follows: the average of gene expression level among the CSCs, the gene expression level of hiPSC 201B7, and the SD of the gene expression level among the CSCs, respectively. These values were calculated with I , which was described in the “Materials and methods” section. ( C ) Average + 2SD was calculated with the max–min value. These values were calculated with Bioconductor normalized intensity for each gene. Normalized intensity i’ was shown in base-2 logarithm on Y-axis. For , a gene set was made by only one parameter ( b ). To list up genes that have much difference, parameter ( C ) in addition to ( b ) was used for each gene set of – . Using each gene set, sSOM analysis was performed with I .

Article Snippet: For iPS-CC1 and iPS-GC1, the microarray study was carried out using a Whole Human Genome Oligo Microarray 4×44 K (Agilent Technologies).

Techniques: Microarray, Selection, Expressing

Journal: Cancer Informatics

Article Title: Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map

doi: 10.4137/CIN.S39839

Figure Lengend Snippet: Mapping and clustering of normal hiPS and all the CSCs with sSOM. Microarray data of hiPSC 201B7 were obtained from NCBI GEO (GSM241846), and those of the CSCs were obtained as our original data. Notes: ( A ) Gene expression patterns were analyzed by sSOM with the microarray data of GSM241846 and the CSCs. The data were used 2678 probes, which were extracted by |A-G|-2V > 0. ( b ) Each of the CSCs and hiPSC 201B7 was mapped on a sphere by sSOM analysis. The CSCs were clustered into three groups with sSOM. Each of analyzed CSCs was depicted on a sphere. The CSCs named in red color were mapped on the front side of the sphere. The CSCs named in light blue color were mapped on the back side of the sphere.

Article Snippet: For iPS-CC1 and iPS-GC1, the microarray study was carried out using a Whole Human Genome Oligo Microarray 4×44 K (Agilent Technologies).

Techniques: Microarray, Expressing

Journal: Cancer Informatics

Article Title: Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map

doi: 10.4137/CIN.S39839

Figure Lengend Snippet: Mapping and comparison of normal hiPSC and iPS-CC1 cells with sSOM. Notes: ( A ) Gene expression patterns analyzed by sSOM with the microarray data of 201B7 (GSM241846) and iPS-CC1. The data were used 598 genes, which were extracted by the two parameters (see ). Each of iPS-CC1 was mapped as a sphere by sSOM analysis. The normalized intensities of 323 upregulating genes ( b ) or 275 downregulating genes ( C ) in iPS-CC1, which were compared to GSM241846, were analyzed by sSOM. Ten genes close to the IP were aligned by the order of NSD as listed in and . Graphs were depicted as mean + SD. Normalized intensity i’ was shown in base-2 logarithm on Y-axis. Y-linked genes were eliminated from the list because sex differences were confounding factor.

Article Snippet: For iPS-CC1 and iPS-GC1, the microarray study was carried out using a Whole Human Genome Oligo Microarray 4×44 K (Agilent Technologies).

Techniques: Expressing, Microarray

Journal: Cancer Informatics

Article Title: Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map

doi: 10.4137/CIN.S39839

Figure Lengend Snippet: Mapping and comparison of normal hiPSC and iPS-GC1 with sSOM. Notes: ( A ) Gene expression patterns analyzed by sSOM with the microarray data of 201B7 (GSM251846) and iPS-GC1. The data were used 439 genes, which were extracted by the two parameters (see ). Each of iPS-GC1 was mapped as a sphere by sSOM analysis. The normalized intensities of 328 upregulating genes ( b ) or 111 downregulating genes ( C ) of iPS-GC1, which were compared to GSM241846, were analyzed by sSOM, and 10 genes close to the IP were aligned by the order of NSD as listed in and . Graphs are depicted as mean + SD. Normalized intensity i’ was shown in base-2 logarithm on Y-axis. Y-linked genes were eliminated from the list because sex differences were confounding factor.

Article Snippet: For iPS-CC1 and iPS-GC1, the microarray study was carried out using a Whole Human Genome Oligo Microarray 4×44 K (Agilent Technologies).

Techniques: Expressing, Microarray

Journal: Cancer Informatics

Article Title: Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map

doi: 10.4137/CIN.S39839

Figure Lengend Snippet: Mapping and comparison of normal hiPSC and OCC-hiPS with sSOM. Notes: ( A ) Gene expression patterns analyzed by sSOM with the microarray data of 201B7 (GSM241846) and OCC-hiPS. The data were used 402 genes, which was extracted by the two parameters (see ). Each of OCC-hiPS was mapped as a sphere by sSOM analysis. The normalized intensities of 255 upregulating genes ( b ) or 147 downregulating genes ( C ) of OCC-hiPS, which were compared to GSM241826, were analyzed by sSOM. Ten genes close to the IP were aligned by the order of NSD as listed in and . Graphs were depicted as mean + SD. Normalized intensity i’ was shown in base-2 logarithm on Y-axis.

Article Snippet: For iPS-CC1 and iPS-GC1, the microarray study was carried out using a Whole Human Genome Oligo Microarray 4×44 K (Agilent Technologies).

Techniques: Expressing, Microarray

Journal: PLoS ONE

Article Title: Derivation of iPSCs after Culture of Human Dental Pulp Cells under Defined Conditions

doi: 10.1371/journal.pone.0115392

Figure Lengend Snippet: Scatter plots compared the embryonic stem cell marker genes expression between chemically defined culture conditions (MSCGM-CD) and normal culture conditions (MSCGM) determined by DNA microarray. The green lines indicate the diagonal and 2-fold changes between the two samples. Black and red circles indicate the expression levels of some embryonic stem cell marker genes .

Article Snippet: Following labeling and clean-up, the cDNAs were quantified using an ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE) and hybridized with a whole human genome 4×44 K oligo-DNA microarray (Agilent Technologies).

Techniques: Marker, Expressing, Microarray