Journal: F1000Research

Article Title: Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker

doi: 10.12688/f1000research.126721.2

Figure Lengend Snippet: List of online resources employed for profiling CEACAM6 literature/transcriptional data, including those generated as part of the present work.

Article Snippet: Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.

Techniques: Generated, Derivative Assay, Biomarker Discovery, Quantitative Proteomics, Gene Expression, Expressing

Journal: F1000Research

Article Title: Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker

doi: 10.12688/f1000research.126721.2

Figure Lengend Snippet: A. The module fingerprint heatmap represents the proportion of transcript for a given module (rows) for which abundance levels are significantly different in case subjects compared to the respective controls for a given reference dataset (columns). Values can range from +100% (solid red: abundance for all constitutive transcripts for the module are significantly higher) to −100% (solid blue: abundance for all constitutive transcripts for the module are significantly lower). Responses are shown for four modules included in the module aggregate A38 from the BloodGen3 repertoire, including module M10.4 from which CEACAM6 was selected. B. The box plot represents the percentage response averaged for module M10.4, across the 16 reference datasets (we have contributed this dataset collection to GEO as part of an earlier work, and it is accessible under accession number GSE100150. Plots were generated using the BloodGen3 web application: https://drinchai.shinyapps.io/BloodGen3Module/ .

Article Snippet: Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.

Techniques: Generated

Journal: F1000Research

Article Title: Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker

doi: 10.12688/f1000research.126721.2

Figure Lengend Snippet: List of the most prevalent diseases/physiological states and cell types found among the CEACAM6 literature.

Article Snippet: Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.

Techniques:

Journal: F1000Research

Article Title: Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker

doi: 10.12688/f1000research.126721.2

Figure Lengend Snippet: The prevalence of articles among the literature associated with CEACAM6 for disease entities (A) or cell type entities (B) are represented by circles of different sizes and colors, corresponding to the number of associated articles. It is possible to access underlying information by zooming into each of the circles. The Prezi presentation can be accessed at this url: https://prezi.com/view/pQ7TKEC6tgY3cuik9ckt/ Step 3: background literature profiling.

Article Snippet: Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.

Techniques:

Journal: F1000Research

Article Title: Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker

doi: 10.12688/f1000research.126721.2

Figure Lengend Snippet: Published reports describing CEACAM6 as being of clinical relevance as a biomarker.

Article Snippet: Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.

Techniques: Biomarker Discovery, Marker

Journal: F1000Research

Article Title: Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker

doi: 10.12688/f1000research.126721.2

Figure Lengend Snippet: Pathological, immunological, or physiological states where CEACAM6 transcript abundance levels have been found to differ in cases vs controls.

Article Snippet: Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.

Techniques: Control, Infection

Journal: F1000Research

Article Title: Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker

doi: 10.12688/f1000research.126721.2

Figure Lengend Snippet: This violin plot shows the fold change in abundance of CEACAM6 mRNA measured by RNA sequencing in the blood of human subjects across 16 reference disease cohorts, compared to their respective control subjects. In total blood transcriptome of 985 subjects was profiled. For details, see original work by Altman, Rinchai et al . GEO deposition: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100150 ; plot: https://chart-studio.plotly.com/create/?fid=dchaussabel%3A132 interactive version with values expressed as counts: http://cd2k.gxbsidra.org/dm3/miniURL/view/NH .

Article Snippet: Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.

Techniques: RNA Sequencing, Control

Journal: F1000Research

Article Title: Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker

doi: 10.12688/f1000research.126721.2

Figure Lengend Snippet: This box plot shows levels of abundance of CEACAM6 RNA measured by RNA sequencing in neutrophils, monocytes, B-cells, CD4+ T-cells, CD8+ T-cells and NK cells purified from the blood of human subjects, including patients with ALS, type 1 diabetes, multiple sclerosis (immediately before and 24 hours after initiation of beta interferon therapy) or sepsis and healthy controls. Values are normalized to the median calculated across all conditions. For details, see original work by Linsley et al . GEO deposition: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60424 plot: https://plotly.com/~dchaussabel/171/ .

Article Snippet: Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.

Techniques: RNA Sequencing, Purification

Journal: F1000Research

Article Title: Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker

doi: 10.12688/f1000research.126721.2

Figure Lengend Snippet: This tSNE plot shows abundance levels of CEACAM6 measured by single-cell RNA sequencing among dissociated metastatic prostate tumor tissue cells. After quality control, this set consisted of 2,170 cells obtained from 14 patients and 15 biopsies. Clusters are labelled for dominant cell type based on marker gene expression on the plot above. Normalized transcript per million (TPM) counts for CEACAM6 are shown in blue on the plot below. For details, see original work by He et al . An interactive version of this plot is accessible via the Broad Institute single cell portal: https://singlecell.broadinstitute.org/single_cell/study/SCP1244/transcriptional-mediators-of-treatment-resistance-in-lethal-prostate-cancer?genes=CEACAM6#study-visualize .

Article Snippet: Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.

Techniques: RNA Sequencing, Control, Marker, Gene Expression

Journal: F1000Research

Article Title: Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker

doi: 10.12688/f1000research.126721.2

Figure Lengend Snippet: The box plot represents transcript abundance levels for the CEACAM6 gene in blood samples obtained from four healthy donors, cultivated for 6 hours at 37°C in the presence of pathogens, as well as pathogen-derived and host-derived immune stimuli (HKAL=heat-killed Acholeplasma laidlawii , HKLP=heat-killed Legionella pneumophila , HKSA=heat-killed Staphylococcus aureus , Flu=live influenza A virus, RSV=live respiratory syncytial virus). For details, see original work by Obermoser et al . GEO deposition: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30101 plot: https://plotly.com/~dchaussabel/173/ .

Article Snippet: Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.

Techniques: Derivative Assay, Virus

Journal: F1000Research

Article Title: Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker

doi: 10.12688/f1000research.126721.2

Figure Lengend Snippet: Published gene signatures comprising CEACAM6. This table lists targeted gene sets or gene panels comprising CEACAM6. Lists of differentially expressed genes that consists of tens or hundreds of transcripts are purposedly omitted.

Article Snippet: Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.

Techniques: