Tag: SKCM
Comprehensive analysis of necroptotic patterns and associated immune landscapes in individualized treatment of skin cutaneous melanoma
Identification of the SKCM necroptosis cluster The comprehensive analysis encompassed a total of 803 patients drawn from five distinct melanoma cohorts, namely, TCGA-SKCM, GSE65094, GSE53118, GSE54467, and GSE19234. Employing an unsupervised clustering algorithm, we stratified melanoma patients based on their NRG expression profiles. This facilitated a deeper exploration of the…
Construction of a novel prognostic model in skin cutaneous melanoma based on chemokines-related gene signature
Skin cutaneous melanoma, SKCM, is one of the most aggressive treatment-resistant tumours. Despite the fact that the BRAF oncogene and immunological checkpoints such as PD-1/PD-L1 and CTLA-4 have enhanced the therapeutic efficacy of SKCM, the subsequent resistance mechanisms and remedies have raised concerns. Chemokines have a significant role in the…
PHF5A is a potential diagnostic, prognostic, and immunological biomarker in pan-cancer
PHF5A expression analysis Figure 1A demonstrated that PHF5A expression level was compared between tumor and corresponding normal tissues using TIMER2 tool. As compared to normal tissues, PHF5A expression was considerably elevated in Bladder urothelial carcinoma (BLCA), Breast invasive carcinoma (BRCA), Cholangiocarcinoma (CHOL), Colon adenocarcinoma (COAD), Esophageal carcinoma (ESCA), Head and neck…
Characterization of prognosis and immune infiltration by a novel glutamine metabolism-related model in cutaneous melanoma
Open Access ARTICLE MENGQIN ZHU1,2,3,4,#, TIANYI XU5,#, HAN ZHANG3,4, XIN FAN3,4, YULAN WANG6, JIAJIA ZHANG3,4, FEI YU1,2,3,4,* 1 Shanghai Clinical College, Anhui Medical University, Shanghai, 200040, China2 The Fifth Clinical Medical College, Anhui Medical University, Hefei, 230032, China3 Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of…
TNFSF10, an autophagy related gene, was a prognostic and immune infiltration marker in skin cutaneous melanoma
Autophagy exerts a pivotal effect on skin cutaneous melanoma (SKCM). This study was aimed to investigate the expression of autophagy related genes (ARGs) in SKCM as well as its clinical value. Differentially expressed (DE) ARGs were downloaded from the intersection of SKCM data in GEPIA2 database and ARGs in Human…
Inhibition of tumor intrinsic BANF1 activates antitumor immune responses via cGAS-STING and enhances the efficacy of PD-1 blockade
Introduction Immune checkpoint inhibitors (ICIs) have revolutionized the treatment pattern of various cancers, including melanoma and non-small cell lung cancer (NSCLC).1–3 However, there are still a considerable proportion (40%–60%) of patients who do not respond or do not achieve durable responses to these drugs.4 Thus, it is urgent clinical need…
CACNA1C mutation as a prognosis predictor of immune checkpoint inhibitor in skin cutaneous melanoma
doi: 10.2217/imt-2022-0175. Online ahead of print. Affiliations Expand Affiliations 1 Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China. 2 The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China. Item in Clipboard Yushan Huang et al. Immunotherapy. 2023. Show details Display options…
Bioinformatics analysis of hedgehog interacting protein in colorectal cancer: a study based on GEO data and TCGA data | BMC Gastroenterology
HHIP was lowly expressed in CRC tissues and HHIP expression was associated with cancer patient prognosis We acquired the RNA-sequencing data of CRC from TCGA public database. To pursue possible roles of HHIP in carcinostasis, we first analyzed HHIP expression in 33 types of human cancers. As shown in Fig. 1A,…
Pan-cancer structurome reveals overrepresentation of beta sandwiches and underrepresentation of alpha helical domains
AlphaFold models significantly expanded structural space of over and underexpressed protein-coding genes in 21 cancer types Our non-redundant sets of over and underexpressed protein-coding genes for all cancer types include 5341 and 7320 genes, respectively. Figure 1A, B illustrates the availability of known 3D structures (PDB) and AlphaFold models (AF). For…
Construction and Identification of an NLR-Associated Prognostic Signature Revealing the Heterogeneous Immune Response in Skin Cutaneous Melanoma,Clinical, Cosmetic and Investigational Dermatology
Background: Skin cutaneous melanoma (SKCM) is the deadliest dermatology tumor. Ongoing researches have confirmed that the NOD-like receptors (NLRs) family are crucial in driving carcinogenesis. However, the function of NLRs signaling pathway-related genes in SKCM remains unclear.Objective: To establish and identify an NLRs-related prognostic signature and to explore its predictive…
Construction & ID of an NLRs-associated Prognostic Signature
Introduction Skin cutaneous melanoma (SKCM) is the most severe dermatologic malignancy, and its incidence has increased worldwide in recent years.1 SKCM accounts for 1% of all skin cancer patients, yet it is responsible for roughly 80% of all skin cancer deaths.2 Early-stage SKCM (localized or regional) can be surgically removed,…
Identification and validation of TME-related signatures to predict prognosis and response to anti-tumor therapies in skin cutaneous melanoma
The tumor microenvironment (TME) dynamically regulates cancer progression and affects clinical outcomes. This study aimed to identify molecular subtypes and construct a prognostic risk model based on TME-related signatures in skin cutaneous melanoma (SKCM) patients. We categorized SKCM patients based on transcriptome data of SKCM from The Cancer Genome Atlas…
Comprehensive prediction of immune microenvironment and hot and cold tumor differentiation in cutaneous melanoma based on necroptosis-related lncRNA
Identify necroptosis-related lncRNAs in SKCM There are 386 necroptosis-related lncRNAs identified from the data of TCGA and GTEx, as the standard is the coefficients > 0.4 and P < 0.001. After that, flowing the differential expression analysis, 87 necroptosis-related lncRNAs were found to display significantly differential expression with the screen value as |logFC…
Analysis of differential gene immune infiltration and clinical characteristics of skin cutaneous melanoma based on systems biology and drug repositioning methods to identify drug candidates for skin cutaneous melanoma
Skin cutaneous melanoma (SKCM) has a low early detection rate and a high mortality rate. There are many problems such as side effects and drug resistance in existing therapeutic drugs. Current studies have confirmed that SKCM pathogenesis-related genes promote the invasion and metastasis of cutaneous melanoma, but their roles in…
Researchers discover pathway critical for lymphoma development
Activation of the polyamine-hypusine circuit is a hallmark of human cancer and of MYC-driven lymphoma. A, Copy number alterations (CNA) of EIF5A and EIFA2 (left), and of DHPS and DOHH (right) across different cancer types. Abbreviations for the indicated TCGA datasets are: prostate = PRAD; Liver Hepatocellular = LIHC; Diffuse…
Pan-cancer analysis reveals IGFL2 as a potential target for cancer prognosis and immunotherapy
Expression of IGFL2 in cancer According to the TIMER2.0 database results, the difference in IGFL2 expression between cancer and normal tissues was significant in most cancers, including BLCA, BRCA, CHOL, COAD, ESCA, GBM, HNSC, KIRC, KIRP, LIHC, LUAD, LUSC, SKCM, HNSC, STAD THCA, and UCEC, while IGFL2 expression was higher…
A pan-cancer analysis of DDR1 in prognostic signature and tumor immunity, drug resistance
Differential expression of DDR1 between tumor and normal tissue samples To better understand DDR1 expression levels in various cancer types, we first performed a pan-cancer analysis of 33 cancers in the TCGA database. Excluding cancers without corresponding normal samples, significant differences in DDR1 expression were found between tumor and normal…
Anyone familiar with ICGC’s DCC data releases?
Anyone familiar with ICGC’s DCC data releases? 0 Hi all, As part of my project, I wanted to find recurrent somatic mutations in cancer, but not only coding regions, I want to assess the whole genome for noncoding somatic mutations -> Thus I need WGS data. My supervisor directed me…
SLC25A13 Could Be Prognostic, Therapeutic Biomarker in Skin Cutaneous Melanoma
The analysis suggests the marker could be used to screen patients for potential immunotherapy. Solute carrier family 25 member 13 (SLC25A13) may be a powerful prognostic biomarker in patients with skin cutaneous melanoma (SKCM), according to new research. The study, published in Disease Markers, showed that patients with SKCM who…
Role of CD68 in tumor immunity and prognosis prediction in pan-cancer
Expression of CD68 in pan-cancer First, to fully clarify the expression of CD68 in pan-cancer, we matched the GTEx normal samples with TCGA tumor samples (Fig. 1A). We found that the levels of CD68 were significantly elevated (P < 0.01) in colon adenocarcinoma (COAD), glioblastoma multiforme (GBM), kidney renal clear cell carcinoma (KIRC),…
Skin cutaneous melanoma properties of immune-related lncRNAs identifying potential prognostic biomarkers
. 2022 Mar 31;14(undefined). doi: 10.18632/aging.203982. Online ahead of print. Affiliations Expand Affiliations 1 Department of Breast Surgery, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, P.R. China. 2 Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, P.R. China. 3…
Thymidine Kinase 1 Drives Skin Cutaneous Melanoma Malignant Progression and Metabolic Reprogramming
Background: Thymidine kinase 1 (TK1) is a cell cycle-dependent kinase that catalyzes the addition of a gamma-phosphate group to thymidine. The protumorigenic role of TK1 has been reported in various malignancies. However, the role of TK1 in skin cutaneous melanoma (SKCM) remains unclear. This study aimed to explore the molecular…
The Identification of Prognostic and Metastatic Alternative Splicing in Skin Cutaneous Melanoma
Skin cutaneous melanoma (SKCM) is a type of highly invasive cancer originated from melanocytes. It is reported that aberrant alternative splicing (AS) plays an important role in the neoplasia and metastasis of many types of cancer. Therefore, we investigated whether ASEs of pre-RNA have such an influence on the prognosis…
Index of /runs/gdc/report_2018_02_16
Name Last modified Size Description Parent Directory – TCGA-ACC.2018_02_16.diced_metadata.tsv 2018-02-16 01:06 250K TCGA-ACC.2018_02_16.high_res.heatmap.png 2018-02-16 01:08 73K TCGA-ACC.2018_02_16.low_res.heatmap.png 2018-02-16 01:08 37K TCGA-ACC.2018_02_16.sample_counts.tsv 2018-02-16 01:06 142 TCGA-BLCA.2018_02_16.diced_metadata.tsv 2018-02-16 01:06 1.2M TCGA-BLCA.2018_02_16.high_res.heatmap.png 2018-02-16 01:08 90K TCGA-BLCA.2018_02_16.low_res.heatmap.png 2018-02-16 01:08 53K TCGA-BLCA.2018_02_16.sample_counts.tsv 2018-02-16 01:06 201 …
How to access WGS files on TCGA for melanoma/SKCM
How to access WGS files on TCGA for melanoma/SKCM 0 I was trying to find WGS files for TCGA-SKCM so I can run WGS files through our pipeline and search for circular DNA elements in melanoma samples. However, looking on the TCGA website for this type of cancer, it’s unclear…
