Journal: Annals of Translational Medicine

Article Title: Seven ferroptosis-specific expressed genes are considered as potential biomarkers for the diagnosis and treatment of cigarette smoke-induced chronic obstructive pulmonary disease

doi: 10.21037/atm-22-1009

Figure Lengend Snippet: Details of GEO COPD data

Article Snippet: The datasets {"type":"entrez-geo","attrs":{"text":"GSE10006","term_id":"10006"}} GSE10006 , {"type":"entrez-geo","attrs":{"text":"GSE11784","term_id":"11784"}} GSE11784 , {"type":"entrez-geo","attrs":{"text":"GSE20257","term_id":"20257"}} GSE20257 , {"type":"entrez-geo","attrs":{"text":"GSE19407","term_id":"19407"}} GSE19407 , and {"type":"entrez-geo","attrs":{"text":"GSE27973","term_id":"27973"}} GSE27973 are located on the {"type":"entrez-geo","attrs":{"text":"GPL570","term_id":"570"}} GPL570 platform [(HG-U133_Plus_2) Affymetrix Human Genome U133 Plus 2.0 Array], while {"type":"entrez-geo","attrs":{"text":"GSE994","term_id":"994"}} GSE994 is located on the {"type":"entrez-geo","attrs":{"text":"GPL96","term_id":"96"}} GPL96 platform [(HG-U133A) Affymetrix Human Genome U133A Array].

Techniques:

Journal: Annals of Translational Medicine

Article Title: A transcriptomic analysis based on aberrant methylation levels revealed potential novel therapeutic targets for nasopharyngeal carcinoma

doi: 10.21037/atm-21-6628

Figure Lengend Snippet: Data information downloaded from the GEO public database

Article Snippet: The study type, accession number, PubMed Unique Identifier (PMID), Platform, sample source, and sample size of these data sets are set out in . table ft1 table-wrap mode="anchored" t5 caption a7 Study type Accession PMID Platform Source Samples NPC Ctrl Expression profiling by array {"type":"entrez-geo","attrs":{"text":"GSE12452","term_id":"12452"}} GSE12452 17119049; 16912175; 22880099 Affymetrix Nasopharyngeal tissue 31 10 Expression profiling by array {"type":"entrez-geo","attrs":{"text":"GSE13597","term_id":"13597"}} GSE13597 19142888 Affymetrix Nasopharyngeal tissue 25 3 Expression profiling by array {"type":"entrez-geo","attrs":{"text":"GSE40290","term_id":"40290"}} GSE40290 NA Capitalbio Nasopharyngeal tissue 25 8 Expression profiling by array {"type":"entrez-geo","attrs":{"text":"GSE53819","term_id":"53819"}} GSE53819 24763226 Agilent Nasopharyngeal tissue 18 18 Expression profiling by array {"type":"entrez-geo","attrs":{"text":"GSE64634","term_id":"64634"}} GSE64634 26246469 Affymetrix Nasopharyngeal tissue 12 4 Expression profiling by high-throughput sequencing {"type":"entrez-geo","attrs":{"text":"GSE118719","term_id":"118719"}} GSE118719 30477559 Illumina Nasopharyngeal tissue 7 4 Expression profiling by high-throughput sequencing {"type":"entrez-geo","attrs":{"text":"GSE68799","term_id":"68799"}} GSE68799 NA Illumina Nasopharyngeal tissue 42 4 Expression profiling by high-throughput sequencing {"type":"entrez-geo","attrs":{"text":"GSE134886","term_id":"134886"}} GSE134886 33931030 HiSeq Nasopharyngeal tissue 3 3 Methylation profiling by array {"type":"entrez-geo","attrs":{"text":"GSE52068","term_id":"52068"}} GSE52068 26443805; 28146149 Illumina Nasopharyngeal tissue 24 24 Methylation profiling by array {"type":"entrez-geo","attrs":{"text":"GSE62336","term_id":"62336"}} GSE62336 25924914 Illumina Nasopharyngeal tissue 25 25 Total 212 103 Open in a separate window GEO, Gene Expression Omnibus. caption a8 Data information downloaded from the GEO public database Gene expression data processing and meta-analysis To check the distribution of the data and whether there were abnormal values before the enrichment and PPI network analyses, we used a 2-dimensional principal component analysis and density plots of the gene counts to check the data, and the results showed that there was good differentiation between the NPC group and the normal control group (see ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 Distribution of gene expression data in NPC group and control group. (A) 2-dimensional principal component analysis; (B) density plot of gene counts.

Techniques: Expressing, Next-Generation Sequencing, Methylation

Journal: Annals of Translational Medicine

Article Title: Immune abnormalities and differential gene expression in the hippocampus and peripheral blood of patients with Alzheimer’s disease

doi: 10.21037/atm-21-4974

Figure Lengend Snippet: GEO microarray datasets

Article Snippet: The study was conducted in accordance with the Declaration of Helsinki (as revised in 2013). table ft1 table-wrap mode="anchored" t5 caption a7 GEO ID Platform Normal-aging sample AD sample Resource {"type":"entrez-geo","attrs":{"text":"GSE1297","term_id":"1297"}} GSE1297 {"type":"entrez-geo","attrs":{"text":"GPL96","term_id":"96"}} GPL96 [HG-U133A] Affymetrix Human Genome U133A Array 9 22 Hippocampus {"type":"entrez-geo","attrs":{"text":"GSE5281","term_id":"5281"}} GSE5281 {"type":"entrez-geo","attrs":{"text":"GPL570","term_id":"570"}} GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array 13 10 Hippocampus {"type":"entrez-geo","attrs":{"text":"GSE63060","term_id":"63060"}} GSE63060 {"type":"entrez-geo","attrs":{"text":"GPL6947","term_id":"6947"}} GPL6947 Illumina HumanHT-12 V3.0 Expression BeadChip 104 145 Peripheral blood {"type":"entrez-geo","attrs":{"text":"GSE63061","term_id":"63061"}} GSE63061 {"type":"entrez-geo","attrs":{"text":"GPL10558","term_id":"10558"}} GPL10558 Illumina HumanHT-12 V4.0 Expression BeadChip 134 139 Peripheral blood Open in a separate window GEO, Gene Expression Omnibus; ID, identification; AD, Alzheimer’s disease. caption a8 GEO microarray datasets Batch normalization and differential expression analysis The multiple dataset analyses were based on different instruments with different handlers or in different groups.

Techniques: Microarray, Expressing

Journal: American Journal of Cancer Research

Article Title: ALDH2 is a prognostic biomarker and related with immune infiltrates in HCC

doi:

Figure Lengend Snippet: Detailed Information of involved datasets in this research

Article Snippet: Detailed information of involved datasets in this research was shown in . table ft1 table-wrap mode="anchored" t5 caption a7 Datasets Contributor(s) Tumor Non-tumor Platform {"type":"entrez-geo","attrs":{"text":"GSE22058","term_id":"22058"}} GSE22058 Burchard J 100 97 Merck/Rosetta Human RSTA Custom Affymetrix 1.0 microarray {"type":"entrez-geo","attrs":{"text":"GSE36376","term_id":"36376"}} GSE36376 Cheol-Keun Park 240 193 Illumina HumanHT-12 V4.0 expression beadchip {"type":"entrez-geo","attrs":{"text":"GSE14520","term_id":"14520"}} GSE14520 Xin Wei Wang 225 220 Affymetrix Human Genome U133A 2.0 Array {"type":"entrez-geo","attrs":{"text":"GSE10143","term_id":"10143"}} GSE10143 Hoshida Y 80 82 Human 6k Transcriptionally Informative Gene Panel for DASL {"type":"entrez-geo","attrs":{"text":"GSE46444","term_id":"46444"}} GSE46444 Chen X 88 48 Illumina Human Whole-Genome DASL HT {"type":"entrez-geo","attrs":{"text":"GSE54236","term_id":"54236"}} GSE54236 Villa E 81 80 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F {"type":"entrez-geo","attrs":{"text":"GSE63898","term_id":"63898"}} GSE63898 Villanueva A 228 168 Affymetrix Human Genome U219 Array {"type":"entrez-geo","attrs":{"text":"GSE76427","term_id":"76427"}} GSE76427 Grinchuk OV 115 52 Illumina HumanHT-12 V4.0 expression beadchip TCGA-HCC TCGA 374 49 RNA-Seq Open in a separate window Detailed Information of involved datasets in this research ALDH2 expression verification There were 8 datasets that met the criterion, as follows: {"type":"entrez-geo","attrs":{"text":"GSE22058","term_id":"22058"}} GSE22058 , {"type":"entrez-geo","attrs":{"text":"GSE36376","term_id":"36376"}} GSE36376 , {"type":"entrez-geo","attrs":{"text":"GSE14520","term_id":"14520"}} GSE14520 , {"type":"entrez-geo","attrs":{"text":"GSE10143","term_id":"10143"}} GSE10143 , {"type":"entrez-geo","attrs":{"text":"GSE46444","term_id":"46444"}} GSE46444 , {"type":"entrez-geo","attrs":{"text":"GSE54236","term_id":"54236"}} GSE54236 , {"type":"entrez-geo","attrs":{"text":"GSE63898","term_id":"63898"}} GSE63898 and {"type":"entrez-geo","attrs":{"text":"GSE76427","term_id":"76427"}} GSE76427 .

Techniques: Microarray, Expressing

Journal: American Journal of Cancer Research

Article Title: ALDH2 is a prognostic biomarker and related with immune infiltrates in HCC

doi:

Figure Lengend Snippet: ALDH2 expression in HCC and adjacent normal tissues was verifed by GEO database and IHC. A-H. The expression of ALDH2 was significantly lower in 1157 cases of HCC than 940 adjacent normal tissues in the eight datasets (GSE22058, GSE36376, GSE14520, GSE10143, GSE46444, GSE54236, GSE63898 and GSE76427). The expression of ALDH2 was explored using an unpaired t-test. I-K. ALDH2 immunohistochemistry in adjacent normal tissues and HCC cancer tissues.

Article Snippet: Detailed information of involved datasets in this research was shown in . table ft1 table-wrap mode="anchored" t5 caption a7 Datasets Contributor(s) Tumor Non-tumor Platform {"type":"entrez-geo","attrs":{"text":"GSE22058","term_id":"22058"}} GSE22058 Burchard J 100 97 Merck/Rosetta Human RSTA Custom Affymetrix 1.0 microarray {"type":"entrez-geo","attrs":{"text":"GSE36376","term_id":"36376"}} GSE36376 Cheol-Keun Park 240 193 Illumina HumanHT-12 V4.0 expression beadchip {"type":"entrez-geo","attrs":{"text":"GSE14520","term_id":"14520"}} GSE14520 Xin Wei Wang 225 220 Affymetrix Human Genome U133A 2.0 Array {"type":"entrez-geo","attrs":{"text":"GSE10143","term_id":"10143"}} GSE10143 Hoshida Y 80 82 Human 6k Transcriptionally Informative Gene Panel for DASL {"type":"entrez-geo","attrs":{"text":"GSE46444","term_id":"46444"}} GSE46444 Chen X 88 48 Illumina Human Whole-Genome DASL HT {"type":"entrez-geo","attrs":{"text":"GSE54236","term_id":"54236"}} GSE54236 Villa E 81 80 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F {"type":"entrez-geo","attrs":{"text":"GSE63898","term_id":"63898"}} GSE63898 Villanueva A 228 168 Affymetrix Human Genome U219 Array {"type":"entrez-geo","attrs":{"text":"GSE76427","term_id":"76427"}} GSE76427 Grinchuk OV 115 52 Illumina HumanHT-12 V4.0 expression beadchip TCGA-HCC TCGA 374 49 RNA-Seq Open in a separate window Detailed Information of involved datasets in this research ALDH2 expression verification There were 8 datasets that met the criterion, as follows: {"type":"entrez-geo","attrs":{"text":"GSE22058","term_id":"22058"}} GSE22058 , {"type":"entrez-geo","attrs":{"text":"GSE36376","term_id":"36376"}} GSE36376 , {"type":"entrez-geo","attrs":{"text":"GSE14520","term_id":"14520"}} GSE14520 , {"type":"entrez-geo","attrs":{"text":"GSE10143","term_id":"10143"}} GSE10143 , {"type":"entrez-geo","attrs":{"text":"GSE46444","term_id":"46444"}} GSE46444 , {"type":"entrez-geo","attrs":{"text":"GSE54236","term_id":"54236"}} GSE54236 , {"type":"entrez-geo","attrs":{"text":"GSE63898","term_id":"63898"}} GSE63898 and {"type":"entrez-geo","attrs":{"text":"GSE76427","term_id":"76427"}} GSE76427 .

Techniques: Expressing, Immunohistochemistry