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selected-GBID Uni-genename Uni-title p value NM_001299 CNN1 Calponin 1, basic, smooth muscle 0.0174 NM_002836 PTPRA Protein tyrosine phosphatase, receptor type, A 0.0256 NM_003380 VIM Vimentin 0.004 NM_033119 NKD1 Naked cuticle homolog 1 (Drosophila) 0.004 NM_052913 KIAA1913 KIAA1913 0.004 NM_005940 MMP11 Matrix metallopeptidase 11 (stromelysin 3) 0.0069 NM_018032 LUC7L LUC7-like (S. cerevisiae) 0.0367 NM_005269 GLI1 Glioma-associated oncogene homolog 1 (zinc finger protein) 0.0174 BE463997 ARL9 ADP-ribosylation factor-like 9 0.0367 NM_015939 CGI-09 CGI-09 protein 0.0023 NM_002961 S100A4 S100 calcium binding protein A4 (calcium protein, calvasculin, 0.0324 metastasin, murine placental homolog) NM_003014 SFRP4 Secreted frizzled-related protein 4 0.0005 NM_080759 DACH1 Dachshund homolog 1 (Drosophila) 0.004 NM_053042 KIAA1729 KIAA1729 protein 0.004 BX415194 MGC16121 Hypothetical protein MGC16121 0.0367 NM_182734 PLCB1 Phospholipase C, beta 1 (phosphoinositide-specific) 0.0023 NM_006643 SDCCAG3 Serologically defined colon cancer antigen 3 0.011 NM_000088 COL1A1 Collagen, type I, alpha 1 0.0174 NM_033292 CASP1 Caspase 1, apoptosis-related cysteine peptidase 0.0367 (interleukin 1, beta, convertase) NM_003956 CH25H Cholesterol 25-hydroxylase 0.0256 NM_144658 DOCK11 Dedicator of cytokinesis 11 0.011 AK024935 NODATA CDNA: FLJ21283 fis, clone COL01910 0.0363 AL050227 PTGER3 Prostaglandin E receptor 3 (subtype EP3) 0.0367 NM_012383 OSTF1 Osteoclast stimulating factor 1 0.0023 NM_145040 PRKCDBP Protein kinase C, delta binding protein 0.0069 NM_000089 COL1A2 Collagen, type I, alpha 2 0.0174 NM_017671 C20orf42 Chromosome 20 open reading frame 42 0.0174 NM_016522 HNT Neurotrimin 0.0023 NM_032348 MXRA8 Matrix-remodelling associated 8 0.0174 BX537600 PXK PX domain containing serine/threonine kinase 0.0174 NM_021156 DJ971N18.2 Thioredoxin domain containing 13 0.0011 NM_015345 DAAM2 Dishevelled associated activator of morphogenesis 2 0.0367 NM_002474 MYH11 Myosin, heavy polypeptide 11, smooth muscle 0.004 BX538242 FOXP1 Forkhead box P1 0.0256 NM_017885 HCFC1R1 Host cell factor C1 regulator 1 (XPO1 dependent) 0.0256 NM_002592 PCNA Proliferating cell nuclear antigen 0.0367 NM_006385 ZNF211 Zinc finger protein 211 0.0367 NM_003247 THBS2 Thrombospondin 2 0.0023 NM_017577 DKFZp434C032 GRAM domain containing 1C 0.0174 NM_003092 SNRPB2 Small nuclear ribonucleoprotein polypeptide B'' 0.0367 NM_001008489 MGC2610 Kelch-like 23 (Drosophila) 0.011 NODATA NODATA NODATA 0.004 AK129753 NODATA CDNA FLJ26242 fis, clone DMC00770 0.0023 NM_032012 C9orf5 Chromosome 9 open reading frame 5 0.0256 AI935586 NODATA Transcribed locus 0.0256 NM_000311 PRNP Prion protein (p27-30) (Creutzfeld-Jakob disease, 0.011 Gerstmann-Strausler-Scheinker syndrome, fatal familial insomnia) NM_030582 COL18A1 Collagen, type XVIII, alpha 1 0.0174 NM_001920 DCN Decorin 0.0367 NM_004143 CITED1 Cbp/p300-interacting transactivator, 0.0256 with Glu/Asp-rich carboxy-terminal domain, 1 NM_001009924 C20orf30 Chromosome 20 open reading frame 30 0.0021 NM_016100 NAT5 N-acetyltransferase 5 (ARD1 homolog, S. cerevisiae) 0.0023 NM_023074 FLJ12644 Zinc finger protein 649 0.0256 NM_015469 NIPSNAP3A Nipsnap homolog 3A (C. elegans) 0.0256 NM_003451 ZNF177 Zinc finger protein 177 0.0367 NM_001614 ACTG1 Actin, gamma 1 0.0256 NM_001851 COL9A1 Collagen, type IX, alpha 1 0.0367 NM_078487 CDKN2B Cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) 0.0367 NM_006475 POSTN Periostin, osteoblast specific factor 0.011 NM_002290 LAMA4 Laminin, alpha 4 0.0174 NM_016569 TBX3 T-box 3 (ulnar mammary syndrome) 0.0174 NM_007361 NID2 Nidogen 2 (osteonidogen) 0.0256 NODATA NODATA NODATA 0.0367 NM_007001 SLC35D2 Solute carrier family 35, member D2 0.0367 NM_006814 PSMF1 Proteasome (prosome, macropain) inhibitor subunit 1 (PI31) 0.0366 NM_003862 FGF18 Fibroblast growth factor 18 0.0174 NM_001763 CD1A CD1a antigen 0.0367 NM_016081 KIAA0992 Palladin, cytoskeletal associated protein 0.011 NM_006486 FBLN1 Fibulin 1 0.0367 NM_001003845 SP5 Sp5 transcription factor 0.0011 BM686321 NODATA Transcribed locus 0.011 NM_014286 FREQ Frequenin homolog (Drosophila) 0.0256 NM_199341 LOC374920 Hypothetical protein LOC374920 0.0367 AB209354 GLI2 GLI-Kruppel family member GLI2 0.0174 NM_015653 RIBC2 RIB43A domain with coiled-coils 2 0.0069 NM_003122 SPINK1 Serine peptidase inhibitor, Kazal type 1 0.0021 NM_004415 DSP Desmoplakin 0.0174 NM_013248 NXT1 NTF2-like export factor 1 0.0256 NM_004460 FAP Fibroblast activation protein, alpha 0.0367 CF529290/CA43985DNM3 / PIGC Dynamin 3 / Phosphatidylinositol glycan, class C 0.0256 NM_145015 MRGPRF MAS-related GPR, member F 0.0023 NM_024704 C20orf23 Chromosome 20 open reading frame 23 0.0174 NM_003389 CORO2A Coronin, actin binding protein, 2A 0.0256 NM_207333 LOC162967 Zinc finger protein like 0.0256 selected-GBID Uni-genename Uni-title NM_003379 VIL2 Villin 2 (ezrin) NM_002201 ISG20 Interferon stimulated exonuclease gene 20kDa AK000850 NEDD9 Neural precursor cell expressed, developmentally down-regulated 9 BC059408 OVOL1 Ovo-like 1(Drosophila) NM_000493 COL10A1 Collagen, type X, alpha 1(Schmid metaphyseal chondrodysplasia) NM_006895 HNMT Histamine N-methyltransferase NM_001025071RPS14 Ribosomal protein S14 NM_020125 SLAMF8 SLAM family member 8 NM_007350 PHLDA1 Pleckstrin homology-like domain, family A, member 1 NM_001010971SAMD13 Sterile alpha motif domain containing 13 NM_173075 APBB2 Amyloid beta (A4) precursor protein-binding, family B, member 2 (Fe65-like) NM_000174 GP9 Glycoprotein IX (platelet) NM_019594 LRRC8A Leucine rich repeat containing 8 family, member A AK021777 GALNT10 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10) NM_021197 WFDC1 WAP four-disulfide core domain 1 NM_138409 C6orf117 Chromosome 6 open reading frame 117 NM_017450 BAIAP2 BAI1-associated protein 2 NM_152392 AHSA2 AHA1, activator of heat shock 90kDa protein ATPase homolog 2 (yeast) NM_138768 MYEOV Myeloma overexpressed gene (in a subset of t(11;14) positive multiple myelomas) NM_033200 TMEM153 Transmembrane protein 153 BQ067788 LOC339290 Hypothetical protein LOC339290 NM_019044 CCDC93 Coiled-coil domain containing 93 NM_012338 TSPAN12 Tetraspanin 12 NM_001017402LAMB3 Laminin, beta 3 NM_001001396ATP2B4 ATPase, Ca++ transporting, plasma membrane 4 NM_145285 NKX2-3 NK2 transcription factor related, locus 3 (Drosophila) NM_002964 S100A8 S100 calcium binding protein A8 NM_019035 PCDH18 Protocadherin 18 NM_080759 DACH1 Dachshund homolog 1 (Drosophila) NM_000453 SLC5A5 Solute carrier family 5 (sodium iodide symporter), member 5 NM_016614 TTRAP TRAF and TNF receptor associated protein XM_032901/XM_936700KIAA0226 / NODATAKIAA0226 / NODATA BM141825 NODATA Transcribed locus BM980591 NODATA Transcribed locus NM_152597 FSIP1 Fibrous sheath interacting protein 1 NM_002988 CCL18 Chemokine (C-C motif) ligand 18 (pulmonary and activation-regulated) NM_007063 TBC1D8 TBC1 domain family, member 8 (with GRAM domain) NM_005623 CCL8 Chemokine (C-C motif) ligand 8 NM_024861 FLJ22671 Hypothetical protein FLJ22671 NM_003956 CH25H Cholesterol 25-hydroxylase NM_017784 OSBPL10 Oxysterol binding protein-like 10 NM_007329 DMBT1 Deleted in malignant brain tumors 1 NM_002404 MFAP4 Microfibrillar-associated protein 4 NM_001010924C10orf38 Chromosome 10 open reading frame 38 NM_001037171ACOT9 Acyl-CoA thioesterase 9 NM_005110 GFPT2 Glutamine-fructose-6-phosphate transaminase 2 NM_003617 RGS5 Regulator of G-protein signalling 5 NM_004994 MMP9 Matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) NM_004848 C1orf38 Chromosome 1 open reading frame 38 NM_006419 CXCL13 Chemokine (C-X-C motif) ligand 13 (B-cell chemoattractant) AA766831 RAD50 RAD50 homolog (S. cerevisiae) BX648185 EXOD1 Exonuclease domain containing 1 NM_173843 IL1RN Interleukin 1 receptor antagonist NM_000967 RPL3 Ribosomal protein L3 CA426758 KNS2 Kinesin 2 NM_001565 CXCL10 Chemokine (C-X-C motif) ligand 10 AK021529 FBXL18 F-box and leucine-rich repeat protein 18 NM_147780 CTSB Cathepsin B NM_207380 FLJ43339 FLJ43339 protein NM_014314 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 AA158795/AK122903NODATA / EPS8L2Transcribed locus / EPS8-like 2 NM_000201 ICAM1 Intercellular adhesion molecule 1 (CD54), human rhinovirus receptor NM_003255/XM_001132362TIMP2 / NODATATIMP metallopeptidase inhibitor 2 / NODATA NM_003262 TLOC1 Translocation protein 1 NM_001511 CXCL1 Chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha) NM_021239 RBM25 RNA binding motif protein 25 NM_000186 CFH Complement factor H NM_000916 OXTR Oxytocin receptor XM_001125745ZNF469 Zinc finger protein 469 NM_032895 MGC14376 Hypothetical protein MGC14376 NM_014465 SULT1B1 Sulfotransferase family, cytosolic, 1B, member 1 NM_015550 OSBPL3 Oxysterol binding protein-like 3 NM_001012 RPS8 Ribosomal protein S8 AB014592 KIAA0692 KIAA0692 NM_022484 TMEM168 Transmembrane protein 168 NM_002112 HDC Histidine decarboxylase NM_014178 STXBP6 Syntaxin binding protein 6 (amisyn) NM_006509 RELB V-rel reticuloendotheliosis viral oncogene homolog B, nuclear factor of kappa light polypeptide gene enhancer in B-cells 3 (avian) XM_290527 USP35 Ubiquitin specific peptidase 35 NM_080881 DBN1 Drebrin 1 NM_003348 UBE2N Ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast) NM_144970 CXorf38 Chromosome X open reading frame 38 NM_138410 CMTM7 CKLF-like MARVEL transmembrane domain containing 7 NM_006533 MIA Melanoma inhibitory activity NM_003344 UBE2H Ubiquitin-conjugating enzyme E2H (UBC8 homolog, yeast) NM_080546 SLC44A1 Solute carrier family 44, member
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    Wang et al. J Transl Med (2020) 18:67 https://doi.org/10.1186/s12967-020-02255-6 Journal of Translational Medicine RESEARCH Open Access Development and validation of a novel immune-related prognostic model in hepatocellular carcinoma Zheng Wang1, Jie Zhu1, Yongjuan Liu3, Changhong Liu2, Wenqi Wang2, Fengzhe Chen1* and Lixian Ma1* Abstract Background: Growing evidence has suggested that immune-related genes play crucial roles in the development and progression of hepatocellular carcinoma (HCC). Nevertheless, the utility of immune-related genes for evaluating the prognosis of HCC patients are still lacking. The study aimed to explore gene signatures and prognostic values of immune-related genes in HCC. Methods: We comprehensively integrated gene expression data acquired from 374 HCC and 50 normal tissues in The Cancer Genome Atlas (TCGA). Diferentially expressed genes (DEGs) analysis and univariate Cox regression analysis were performed to identify DEGs that related to overall survival. An immune prognostic model was constructed using the Lasso and multivariate Cox regression analyses. Furthermore, Cox regression analysis was applied to identify independent prognostic factors in HCC. The correlation analysis between immune-related signature and immune cells infltration were also investigated. Finally, the signature was validated in an external independent dataset. Results: A total of 329 diferentially expressed immune‐related genes were detected. 64 immune‐related genes were identifed to be markedly related to overall survival in HCC patients using univariate Cox regression analysis. Then we established a TF-mediated network for exploring the regulatory mechanisms of these genes. Lasso and multivariate Cox regression analyses were applied to construct the immune-based prognostic model, which consisted of nine immune‐related genes.
  • Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses

    Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses

    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes.
  • Role of Amylase in Ovarian Cancer Mai Mohamed University of South Florida, Mmohamed@Health.Usf.Edu

    Role of Amylase in Ovarian Cancer Mai Mohamed University of South Florida, [email protected]

    University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School July 2017 Role of Amylase in Ovarian Cancer Mai Mohamed University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the Pathology Commons Scholar Commons Citation Mohamed, Mai, "Role of Amylase in Ovarian Cancer" (2017). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/6907 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Role of Amylase in Ovarian Cancer by Mai Mohamed A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Pathology and Cell Biology Morsani College of Medicine University of South Florida Major Professor: Patricia Kruk, Ph.D. Paula C. Bickford, Ph.D. Meera Nanjundan, Ph.D. Marzenna Wiranowska, Ph.D. Lauri Wright, Ph.D. Date of Approval: June 29, 2017 Keywords: ovarian cancer, amylase, computational analyses, glycocalyx, cellular invasion Copyright © 2017, Mai Mohamed Dedication This dissertation is dedicated to my parents, Ahmed and Fatma, who have always stressed the importance of education, and, throughout my education, have been my strongest source of encouragement and support. They always believed in me and I am eternally grateful to them. I would also like to thank my brothers, Mohamed and Hussien, and my sister, Mariam. I would also like to thank my husband, Ahmed.