{ "title": "Ten Genes", "genes": [ { "mouse": "Wfdc2", "human": "WFDC2", "human_name": "WAP four-disulfide core domain 2", "orthology": { "mgi_id": "MGI:1914951", "mouse_entrez": "67701", "hgnc_id": "HGNC:15939", "ensembl": "ENSG00000101443", "entrez": "10406", "location": "20q13.12", "hgnc_xref_agrees": true, "methods_matched": [ "Ensembl Compara", "HGNC", "OMA", "OrthoFinder", "OrthoInspector", "PANTHER", "PhylomeDB", "SonicParanoid" ], "methods_not_matched": [ "InParanoid", "Hieranoid" ], "other_stringent_human": [] }, "mouse_result": { "A": { "gene": "Wfdc2", "rank_up": 80, "log2fc": 1.97, "padj": 4.02e-225, "pct_in": 0.976, "pct_ref": 0.862, "direction": "up in PDAC", "name": "K5-dominant tumor epithelial clusters (0,1,2,3,7) vs K4-dominant ADM cluster (4)" }, "B": { "gene": "Wfdc2", "rank_up": 243, "log2fc": 1.061, "padj": 9.72e-42, "pct_in": 0.939, "pct_ref": 0.862, "direction": "up in PDAC", "name": "Classical ductal-like cluster 1 vs ADM cluster 4" }, "C": { "gene": "Wfdc2", "rank_up": 56, "log2fc": 2.391, "padj": 7.84e-302, "pct_in": 0.973, "pct_ref": 0.775, "direction": "up in PDAC", "name": "All K5 cells vs all K4 cells" } }, "xena": { "probe": "ENSG00000101443.17", "tumor": { "n": 178, "median_log2": 7.662, "q1_log2": 6.565, "q3_log2": 8.789, "median_tpm": 202.5 }, "gtex_normal": { "n": 167, "median_log2": 2.956, "q1_log2": 2.416, "q3_log2": 3.995, "median_tpm": 7.8 }, "tcga_adjacent_normal": { "n": 4, "median_log2": 7.801, "q1_log2": 4.984, "q3_log2": 8.424, "median_tpm": 223.1 }, "log2_median_diff": 4.706, "mwu_p": 1.64e-52, "auc_tumor_gt_normal": 0.975 }, "hpa": { "rna_tissue_specificity": "Tissue enhanced", "rna_tissue_distribution": "Detected in many", "pancreas_ntpm": 31.7, "duct_ncpm": 191.0, "acinar_ncpm": 12.1, "prog_tcga": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "9.56e-2" }, "prog_validation": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "1.03e-1" }, "page": "https://www.proteinatlas.org/ENSG00000101443-WFDC2/cancer/pancreatic+cancer", "tissue_page": "https://www.proteinatlas.org/ENSG00000101443-WFDC2/tissue", "url": "https://www.proteinatlas.org/api/search_download.php?search=ENSG00000101443&format=json&columns=g,eg,rnats,rnatd,t_RNA_pancreas,sc_RNA_Pancreatic_duct_cells,sc_RNA_Pancreatic_acinar_cells,prognostic_Pancreatic_Adenocarcinoma_(TCGA),prognostic_Pancreatic_Adenocarcinoma_(validation)&compress=no" }, "literature": { "papers": [ { "pmid": "25642754", "title": "Expression and diagnostic value of HE4 in pancreatic adenocarcinoma", "journal": "Int J Mol Sci", "year": "2015", "first_author": "Huang T", "summary": "Found HE4 (the WFDC2 protein) higher in pancreatic adenocarcinoma than in normal or adjacent tissue by qPCR and immunostaining, and higher in patient serum; tested as a blood marker alongside CA19-9.", "cell_resolved_higher": true, "url": "https://pubmed.ncbi.nlm.nih.gov/25642754/" }, { "pmid": "33367933", "title": "High levels of human epididymis protein 4 mRNA and protein expression are associated with chemoresistance and a poor prognosis in pancreatic cancer", "journal": "Int J Oncol", "year": "2021", "first_author": "Ohkuma R", "summary": "In patient-derived xenografts and 80 resected tumors, high HE4 went with chemotherapy resistance and shorter survival.", "cell_resolved_higher": false, "url": "https://pubmed.ncbi.nlm.nih.gov/33367933/" } ], "search_term": "(WFDC2[tiab] OR HE4[tiab]) AND (pancreatic cancer[tiab] OR pancreatic ductal adenocarcinoma[tiab] OR pancreatic adenocarcinoma[tiab] OR PDAC[tiab])", "search_count": 13, "search_retrieved": "2026-10-12" }, "agreement": { "verdict": "agree", "reasons": [ "Mouse: higher in PDAC in all three comparisons (log2FC 1.06 to 2.39, all adjusted p < 0.05).", "Human bulk (Xena): tumor median 202.5 TPM vs normal pancreas 7.8 TPM, log2 difference +4.71, p = 1.6e-52.", "Cell-level human evidence of higher expression in cancer cells: PMID 25642754." ], "note": null } }, { "mouse": "Vim", "human": "VIM", "human_name": "vimentin", "orthology": { "mgi_id": "MGI:98932", "mouse_entrez": "22352", "hgnc_id": "HGNC:12692", "ensembl": "ENSG00000026025", "entrez": "7431", "location": "10p13", "hgnc_xref_agrees": true, "methods_matched": [ "Ensembl Compara", "HGNC", "Hieranoid", "InParanoid", "OMA", "OrthoFinder", "OrthoInspector", "PANTHER", "PhylomeDB", "SonicParanoid" ], "methods_not_matched": [], "other_stringent_human": [] }, "mouse_result": { "A": { "gene": "Vim", "rank_up": 13, "log2fc": 8.274, "padj": 0.0, "pct_in": 0.847, "pct_ref": 0.032, "direction": "up in PDAC", "name": "K5-dominant tumor epithelial clusters (0,1,2,3,7) vs K4-dominant ADM cluster (4)" }, "B": { "gene": "Vim", "rank_up": 33, "log2fc": 4.36, "padj": 1.81e-110, "pct_in": 0.486, "pct_ref": 0.032, "direction": "up in PDAC", "name": "Classical ductal-like cluster 1 vs ADM cluster 4" }, "C": { "gene": "Vim", "rank_up": 12, "log2fc": 7.782, "padj": 0.0, "pct_in": 0.843, "pct_ref": 0.029, "direction": "up in PDAC", "name": "All K5 cells vs all K4 cells" } }, "xena": { "probe": "ENSG00000026025.13", "tumor": { "n": 178, "median_log2": 9.628, "q1_log2": 8.982, "q3_log2": 10.095, "median_tpm": 791.3 }, "gtex_normal": { "n": 167, "median_log2": 7.117, "q1_log2": 6.561, "q3_log2": 7.431, "median_tpm": 138.8 }, "tcga_adjacent_normal": { "n": 4, "median_log2": 10.51, "q1_log2": 10.063, "q3_log2": 10.705, "median_tpm": 1458.2 }, "log2_median_diff": 2.511, "mwu_p": 8.31e-50, "auc_tumor_gt_normal": 0.962 }, "hpa": { "rna_tissue_specificity": "Tissue enhanced", "rna_tissue_distribution": "Detected in all", "pancreas_ntpm": 349.0, "duct_ncpm": 218.1, "acinar_ncpm": 658.3, "prog_tcga": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "6.66e-2" }, "prog_validation": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "3.03e-1" }, "page": "https://www.proteinatlas.org/ENSG00000026025-VIM/cancer/pancreatic+cancer", "tissue_page": "https://www.proteinatlas.org/ENSG00000026025-VIM/tissue", "url": "https://www.proteinatlas.org/api/search_download.php?search=ENSG00000026025&format=json&columns=g,eg,rnats,rnatd,t_RNA_pancreas,sc_RNA_Pancreatic_duct_cells,sc_RNA_Pancreatic_acinar_cells,prognostic_Pancreatic_Adenocarcinoma_(TCGA),prognostic_Pancreatic_Adenocarcinoma_(validation)&compress=no" }, "literature": { "papers": [ { "pmid": "31583548", "title": "Vimentin Expression in Tumor Microenvironment Predicts Survival in Pancreatic Ductal Adenocarcinoma: Heterogeneity in Fibroblast Population", "journal": "Ann Surg Oncol", "year": "2019", "first_author": "Maehira H", "summary": "Looked at vimentin in the tumor stroma of 67 resected PDACs; high vimentin in fibroblasts predicted shorter survival. This is stromal, not tumor-cell, vimentin.", "cell_resolved_higher": false, "url": "https://pubmed.ncbi.nlm.nih.gov/31583548/" }, { "pmid": "40454484", "title": "Polybromo 1/vimentin axis dictates tumor grade, epithelial-mesenchymal transition, and metastasis in pancreatic cancer", "journal": "J Clin Invest", "year": "2025", "first_author": "Kawai M", "summary": "In Kras/p53 mice, losing Pbrm1 raised vimentin and pushed tumors toward a poorly differentiated, metastatic state; in human PDAC, low PBRM1 tracked with high vimentin and worse outcomes.", "cell_resolved_higher": false, "url": "https://pubmed.ncbi.nlm.nih.gov/40454484/" } ], "search_term": "(VIM[tiab] OR vimentin[ti]) AND (pancreatic cancer[tiab] OR pancreatic ductal adenocarcinoma[tiab] OR pancreatic adenocarcinoma[tiab] OR PDAC[tiab])", "search_count": 45, "search_retrieved": "2026-10-12" }, "agreement": { "verdict": "unclear", "reasons": [ "Mouse: higher in PDAC in all three comparisons (log2FC 4.36 to 8.27, all adjusted p < 0.05).", "Human bulk (Xena): tumor median 791.3 TPM vs normal pancreas 138.8 TPM, log2 difference +2.51, p = 8.3e-50.", "No reviewed human study measured it inside cancer cells and found it higher." ], "note": "In the human pancreas, vimentin is a classic fibroblast and stromal marker, and HPA single-cell data rank fibroblasts among its highest cell types. A bulk tumor sample is full of stroma, so the bulk increase cannot be pinned on the cancer cells. Her mouse cells were sorted epithelial cells, which is a different question." } }, { "mouse": "Capg", "human": "CAPG", "human_name": "capping actin protein, gelsolin like", "orthology": { "mgi_id": "MGI:1098259", "mouse_entrez": "12332", "hgnc_id": "HGNC:1474", "ensembl": "ENSG00000042493", "entrez": "822", "location": "2p11.2", "hgnc_xref_agrees": true, "methods_matched": [ "Ensembl Compara", "HGNC", "Hieranoid", "InParanoid", "OMA", "OrthoFinder", "OrthoInspector", "PANTHER", "PhylomeDB", "SonicParanoid" ], "methods_not_matched": [], "other_stringent_human": [] }, "mouse_result": { "A": { "gene": "Capg", "rank_up": 8, "log2fc": 3.127, "padj": 0.0, "pct_in": 0.977, "pct_ref": 0.611, "direction": "up in PDAC", "name": "K5-dominant tumor epithelial clusters (0,1,2,3,7) vs K4-dominant ADM cluster (4)" }, "B": { "gene": "Capg", "rank_up": 6, "log2fc": 2.371, "padj": 3.03e-159, "pct_in": 0.952, "pct_ref": 0.611, "direction": "up in PDAC", "name": "Classical ductal-like cluster 1 vs ADM cluster 4" }, "C": { "gene": "Capg", "rank_up": 9, "log2fc": 3.283, "padj": 0.0, "pct_in": 0.971, "pct_ref": 0.545, "direction": "up in PDAC", "name": "All K5 cells vs all K4 cells" } }, "xena": { "probe": "ENSG00000042493.15", "tumor": { "n": 178, "median_log2": 8.518, "q1_log2": 8.017, "q3_log2": 8.933, "median_tpm": 366.5 }, "gtex_normal": { "n": 167, "median_log2": 3.915, "q1_log2": 3.465, "q3_log2": 4.389, "median_tpm": 15.1 }, "tcga_adjacent_normal": { "n": 4, "median_log2": 8.918, "q1_log2": 8.052, "q3_log2": 9.319, "median_tpm": 483.9 }, "log2_median_diff": 4.603, "mwu_p": 6.28e-51, "auc_tumor_gt_normal": 0.968 }, "hpa": { "rna_tissue_specificity": "Low tissue specificity", "rna_tissue_distribution": "Detected in all", "pancreas_ntpm": 36.6, "duct_ncpm": 65.6, "acinar_ncpm": 27.6, "prog_tcga": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "3.68e-3" }, "prog_validation": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "2.21e-2" }, "page": "https://www.proteinatlas.org/ENSG00000042493-CAPG/cancer/pancreatic+cancer", "tissue_page": "https://www.proteinatlas.org/ENSG00000042493-CAPG/tissue", "url": "https://www.proteinatlas.org/api/search_download.php?search=ENSG00000042493&format=json&columns=g,eg,rnats,rnatd,t_RNA_pancreas,sc_RNA_Pancreatic_duct_cells,sc_RNA_Pancreatic_acinar_cells,prognostic_Pancreatic_Adenocarcinoma_(TCGA),prognostic_Pancreatic_Adenocarcinoma_(validation)&compress=no" }, "literature": { "papers": [ { "pmid": "16847067", "title": "Pancreatic cancer cells overexpress gelsolin family-capping proteins, which contribute to their cell motility", "journal": "Gut", "year": "2007", "first_author": "Thompson CC", "summary": "Immunostaining of benign vs malignant pancreatic ductal cells showed more CapG in malignant cells; knocking it down in cell lines slowed cell movement.", "cell_resolved_higher": true, "url": "https://pubmed.ncbi.nlm.nih.gov/16847067/" }, { "pmid": "41915646", "title": "CAPG serves as a prognostic biomarker and promotes proliferation and migration in pancreatic ductal adenocarcinoma", "journal": "PLoS One", "year": "2026", "first_author": "Qin Z", "summary": "Combined public expression data with patient immunostaining; CAPG was higher in PDAC and higher levels went with worse survival. Knockdown reduced growth and migration in two cell lines.", "cell_resolved_higher": false, "url": "https://pubmed.ncbi.nlm.nih.gov/41915646/" } ], "search_term": "CAPG[tiab] AND (pancreatic cancer[tiab] OR pancreatic ductal adenocarcinoma[tiab] OR pancreatic adenocarcinoma[tiab] OR PDAC[tiab])", "search_count": 4, "search_retrieved": "2026-10-12" }, "agreement": { "verdict": "agree", "reasons": [ "Mouse: higher in PDAC in all three comparisons (log2FC 2.37 to 3.28, all adjusted p < 0.05).", "Human bulk (Xena): tumor median 366.5 TPM vs normal pancreas 15.1 TPM, log2 difference +4.60, p = 6.3e-51.", "Cell-level human evidence of higher expression in cancer cells: PMID 16847067." ], "note": null } }, { "mouse": "Tmsb10", "human": "TMSB10", "human_name": "thymosin beta 10", "orthology": { "mgi_id": "MGI:109146", "mouse_entrez": "19240", "hgnc_id": "HGNC:11879", "ensembl": "ENSG00000034510", "entrez": "9168", "location": "2p11.2", "hgnc_xref_agrees": true, "methods_matched": [ "Ensembl Compara", "HGNC", "Hieranoid", "InParanoid", "OrthoFinder", "OrthoInspector", "PANTHER", "PhylomeDB", "SonicParanoid" ], "methods_not_matched": [ "OMA" ], "other_stringent_human": [] }, "mouse_result": { "A": { "gene": "Tmsb10", "rank_up": 7, "log2fc": 2.724, "padj": 0.0, "pct_in": 1.0, "pct_ref": 0.993, "direction": "up in PDAC", "name": "K5-dominant tumor epithelial clusters (0,1,2,3,7) vs K4-dominant ADM cluster (4)" }, "B": { "gene": "Tmsb10", "rank_up": 22, "log2fc": 1.563, "padj": 2.93e-125, "pct_in": 0.997, "pct_ref": 0.993, "direction": "up in PDAC", "name": "Classical ductal-like cluster 1 vs ADM cluster 4" }, "C": { "gene": "Tmsb10", "rank_up": 8, "log2fc": 2.824, "padj": 0.0, "pct_in": 0.999, "pct_ref": 0.97, "direction": "up in PDAC", "name": "All K5 cells vs all K4 cells" } }, "xena": { "probe": "ENSG00000034510.5", "tumor": { "n": 178, "median_log2": 12.125, "q1_log2": 11.723, "q3_log2": 12.457, "median_tpm": 4466.7 }, "gtex_normal": { "n": 167, "median_log2": 7.981, "q1_log2": 7.554, "q3_log2": 8.508, "median_tpm": 252.6 }, "tcga_adjacent_normal": { "n": 4, "median_log2": 12.16, "q1_log2": 11.68, "q3_log2": 12.435, "median_tpm": 4576.4 }, "log2_median_diff": 4.144, "mwu_p": 1.05e-56, "auc_tumor_gt_normal": 0.994 }, "hpa": { "rna_tissue_specificity": "Low tissue specificity", "rna_tissue_distribution": "Detected in all", "pancreas_ntpm": 844.2, "duct_ncpm": 1497.4, "acinar_ncpm": 1276.0, "prog_tcga": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "2.08e-3" }, "prog_validation": { "is_prognostic": true, "label": "potential prognostic", "type": "unfavorable", "p": "3.89e-4" }, "page": "https://www.proteinatlas.org/ENSG00000034510-TMSB10/cancer/pancreatic+cancer", "tissue_page": "https://www.proteinatlas.org/ENSG00000034510-TMSB10/tissue", "url": "https://www.proteinatlas.org/api/search_download.php?search=ENSG00000034510&format=json&columns=g,eg,rnats,rnatd,t_RNA_pancreas,sc_RNA_Pancreatic_duct_cells,sc_RNA_Pancreatic_acinar_cells,prognostic_Pancreatic_Adenocarcinoma_(TCGA),prognostic_Pancreatic_Adenocarcinoma_(validation)&compress=no" }, "literature": { "papers": [ { "pmid": "19194824", "title": "Thymosin beta-10 is aberrantly expressed in pancreatic cancer and induces JNK activation", "journal": "Cancer Invest", "year": "2009", "first_author": "Li M", "summary": "Thymosin beta-10 was higher in pancreatic cancer tissue and cancer cells than in surrounding normal tissue and normal duct cells; added protein switched on JNK signaling in one cell line.", "cell_resolved_higher": true, "url": "https://pubmed.ncbi.nlm.nih.gov/19194824/" }, { "pmid": "15983444", "title": "Gene expression analysis of pancreatic cell lines reveals genes overexpressed in pancreatic cancer", "journal": "Pancreatology", "year": "2005", "first_author": "Alldinger I", "summary": "A cell line expression screen flagged TMSB10; immunostaining then found it in pancreatic carcinoma but not in non-cancerous pancreas.", "cell_resolved_higher": true, "url": "https://pubmed.ncbi.nlm.nih.gov/15983444/" } ], "search_term": "(TMSB10[tiab] OR \"thymosin beta 10\"[tiab] OR \"thymosin beta-10\"[tiab]) AND (pancreatic cancer[tiab] OR pancreatic ductal adenocarcinoma[tiab] OR pancreatic adenocarcinoma[tiab] OR PDAC[tiab])", "search_count": 3, "search_retrieved": "2026-10-12" }, "agreement": { "verdict": "agree", "reasons": [ "Mouse: higher in PDAC in all three comparisons (log2FC 1.56 to 2.82, all adjusted p < 0.05).", "Human bulk (Xena): tumor median 4466.7 TPM vs normal pancreas 252.6 TPM, log2 difference +4.14, p = 1.1e-56.", "Cell-level human evidence of higher expression in cancer cells: PMID 19194824, 15983444." ], "note": null } }, { "mouse": "S100a6", "human": "S100A6", "human_name": "S100 calcium binding protein A6", "orthology": { "mgi_id": "MGI:1339467", "mouse_entrez": "20200", "hgnc_id": "HGNC:10496", "ensembl": "ENSG00000197956", "entrez": "6277", "location": "1q21.3", "hgnc_xref_agrees": true, "methods_matched": [ "Ensembl Compara", "HGNC", "Hieranoid", "InParanoid", "OMA", "OrthoFinder", "OrthoInspector", "PANTHER", "PhylomeDB", "SonicParanoid" ], "methods_not_matched": [], "other_stringent_human": [] }, "mouse_result": { "A": { "gene": "S100a6", "rank_up": 1, "log2fc": 3.451, "padj": 0.0, "pct_in": 1.0, "pct_ref": 0.986, "direction": "up in PDAC", "name": "K5-dominant tumor epithelial clusters (0,1,2,3,7) vs K4-dominant ADM cluster (4)" }, "B": { "gene": "S100a6", "rank_up": 1, "log2fc": 2.661, "padj": 4.97e-238, "pct_in": 1.0, "pct_ref": 0.986, "direction": "up in PDAC", "name": "Classical ductal-like cluster 1 vs ADM cluster 4" }, "C": { "gene": "S100a6", "rank_up": 2, "log2fc": 4.001, "padj": 0.0, "pct_in": 1.0, "pct_ref": 0.93, "direction": "up in PDAC", "name": "All K5 cells vs all K4 cells" } }, "xena": { "probe": "ENSG00000197956.9", "tumor": { "n": 178, "median_log2": 12.35, "q1_log2": 11.435, "q3_log2": 12.978, "median_tpm": 5220.6 }, "gtex_normal": { "n": 167, "median_log2": 5.741, "q1_log2": 5.196, "q3_log2": 6.341, "median_tpm": 53.5 }, "tcga_adjacent_normal": { "n": 4, "median_log2": 10.705, "q1_log2": 9.808, "q3_log2": 11.143, "median_tpm": 1669.3 }, "log2_median_diff": 6.609, "mwu_p": 2.75e-57, "auc_tumor_gt_normal": 0.997 }, "hpa": { "rna_tissue_specificity": "Low tissue specificity", "rna_tissue_distribution": "Detected in all", "pancreas_ntpm": 297.1, "duct_ncpm": 2725.5, "acinar_ncpm": 1277.6, "prog_tcga": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "4.93e-3" }, "prog_validation": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "1.82e-1" }, "page": "https://www.proteinatlas.org/ENSG00000197956-S100A6/cancer/pancreatic+cancer", "tissue_page": "https://www.proteinatlas.org/ENSG00000197956-S100A6/tissue", "url": "https://www.proteinatlas.org/api/search_download.php?search=ENSG00000197956&format=json&columns=g,eg,rnats,rnatd,t_RNA_pancreas,sc_RNA_Pancreatic_duct_cells,sc_RNA_Pancreatic_acinar_cells,prognostic_Pancreatic_Adenocarcinoma_(TCGA),prognostic_Pancreatic_Adenocarcinoma_(validation)&compress=no" }, "literature": { "papers": [ { "pmid": "15833853", "title": "High nuclear S100A6 (Calcyclin) is significantly associated with poor survival in pancreatic cancer patients", "journal": "Cancer Res", "year": "2005", "first_author": "Vimalachandran D", "summary": "Staining of benign ducts, PanIN lesions and cancer: S100A6 rose with PanIN grade and was strongest in cancer; high nuclear S100A6 went with shorter survival. The closest human match to a PanIN vs PDAC comparison.", "cell_resolved_higher": true, "url": "https://pubmed.ncbi.nlm.nih.gov/15833853/" }, { "pmid": "16278400", "title": "The role of S100A6 in pancreatic cancer development and its clinical implication as a diagnostic marker and therapeutic target", "journal": "Clin Cancer Res", "year": "2005", "first_author": "Ohuchida K", "summary": "Microdissected normal ducts, PanINs and invasive cancer differed in S100A6 levels, and pancreatic juice levels separated cancer from other disease; knockdown reduced invasion in cell lines.", "cell_resolved_higher": true, "url": "https://pubmed.ncbi.nlm.nih.gov/16278400/" }, { "pmid": "17416753", "title": "S100A6 is increased in a stepwise manner during pancreatic carcinogenesis: clinical value of expression analysis in 98 pancreatic juice samples", "journal": "Cancer Epidemiol Biomarkers Prev", "year": "2007", "first_author": "Ohuchida K", "summary": "In microdissected cells and 98 pancreatic juice samples, S100A6 rose stepwise from normal to precursor lesions to cancer.", "cell_resolved_higher": true, "url": "https://pubmed.ncbi.nlm.nih.gov/17416753/" } ], "search_term": "S100A6[tiab] AND (pancreatic cancer[tiab] OR pancreatic ductal adenocarcinoma[tiab] OR pancreatic adenocarcinoma[tiab] OR PDAC[tiab])", "search_count": 29, "search_retrieved": "2026-10-12" }, "agreement": { "verdict": "agree", "reasons": [ "Mouse: higher in PDAC in all three comparisons (log2FC 2.66 to 4.00, all adjusted p < 0.05).", "Human bulk (Xena): tumor median 5220.6 TPM vs normal pancreas 53.5 TPM, log2 difference +6.61, p = 2.8e-57.", "Cell-level human evidence of higher expression in cancer cells: PMID 15833853, 16278400, 17416753." ], "note": "The human studies here include PanIN lesions, so this is the closest human analogue to her PanIN vs PDAC comparison." } }, { "mouse": "Tpi1", "human": "TPI1", "human_name": "triosephosphate isomerase 1", "orthology": { "mgi_id": "MGI:98797", "mouse_entrez": "21991", "hgnc_id": "HGNC:12009", "ensembl": "ENSG00000111669", "entrez": "7167", "location": "12p13.31", "hgnc_xref_agrees": true, "methods_matched": [ "Ensembl Compara", "HGNC", "Hieranoid", "InParanoid", "OMA", "OrthoFinder", "OrthoInspector", "PANTHER", "PhylomeDB", "SonicParanoid" ], "methods_not_matched": [], "other_stringent_human": [] }, "mouse_result": { "A": { "gene": "Tpi1", "rank_up": 17, "log2fc": 2.185, "padj": 0.0, "pct_in": 0.988, "pct_ref": 0.89, "direction": "up in PDAC", "name": "K5-dominant tumor epithelial clusters (0,1,2,3,7) vs K4-dominant ADM cluster (4)" }, "B": { "gene": "Tpi1", "rank_up": 136, "log2fc": 0.896, "padj": 2.13e-57, "pct_in": 0.981, "pct_ref": 0.89, "direction": "up in PDAC", "name": "Classical ductal-like cluster 1 vs ADM cluster 4" }, "C": { "gene": "Tpi1", "rank_up": 15, "log2fc": 2.357, "padj": 0.0, "pct_in": 0.986, "pct_ref": 0.847, "direction": "up in PDAC", "name": "All K5 cells vs all K4 cells" } }, "xena": { "probe": "ENSG00000111669.14", "tumor": { "n": 178, "median_log2": 8.843, "q1_log2": 8.521, "q3_log2": 9.295, "median_tpm": 459.2 }, "gtex_normal": { "n": 167, "median_log2": 6.527, "q1_log2": 6.282, "q3_log2": 6.851, "median_tpm": 92.2 }, "tcga_adjacent_normal": { "n": 4, "median_log2": 8.63, "q1_log2": 8.272, "q3_log2": 8.798, "median_tpm": 396.0 }, "log2_median_diff": 2.316, "mwu_p": 1.1e-55, "auc_tumor_gt_normal": 0.99 }, "hpa": { "rna_tissue_specificity": "Tissue enhanced", "rna_tissue_distribution": "Detected in all", "pancreas_ntpm": 204.0, "duct_ncpm": 574.5, "acinar_ncpm": 316.1, "prog_tcga": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "2.62e-2" }, "prog_validation": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "5.87e-2" }, "page": "https://www.proteinatlas.org/ENSG00000111669-TPI1/cancer/pancreatic+cancer", "tissue_page": "https://www.proteinatlas.org/ENSG00000111669-TPI1/tissue", "url": "https://www.proteinatlas.org/api/search_download.php?search=ENSG00000111669&format=json&columns=g,eg,rnats,rnatd,t_RNA_pancreas,sc_RNA_Pancreatic_duct_cells,sc_RNA_Pancreatic_acinar_cells,prognostic_Pancreatic_Adenocarcinoma_(TCGA),prognostic_Pancreatic_Adenocarcinoma_(validation)&compress=no" }, "literature": { "papers": [ { "pmid": "17332923", "title": "Expression of glycolytic enzymes is increased in pancreatic cancerous tissues as evidenced by proteomic profiling by two-dimensional electrophoresis and liquid chromatography-mass spectrometry/mass spectrometry", "journal": "Int J Oncol", "year": "2007", "first_author": "Mikuriya K", "summary": "A proteomics comparison of 10 tumors with paired non-cancerous tissue found several glycolysis enzymes higher in tumor, including triosephosphate isomerase and GAPDH. Bulk tissue, small sample.", "cell_resolved_higher": false, "url": "https://pubmed.ncbi.nlm.nih.gov/17332923/" }, { "pmid": "39259678", "title": "Identification of TPI1 As a potential therapeutic target in pancreatic cancer with dependency of TP53 mutation using multi-omics analysis", "journal": "Cancer Sci", "year": "2024", "first_author": "Toyoda T", "summary": "In mouse duct organoids, adding p53 loss to mutant Kras ramped up glycolysis; blocking TPI1 slowed growth of human PDAC lines that carry TP53 mutations.", "cell_resolved_higher": false, "url": "https://pubmed.ncbi.nlm.nih.gov/39259678/" } ], "search_term": "(TPI1[tiab] OR \"triosephosphate isomerase\"[tiab]) AND (pancreatic cancer[tiab] OR pancreatic ductal adenocarcinoma[tiab] OR pancreatic adenocarcinoma[tiab] OR PDAC[tiab])", "search_count": 5, "search_retrieved": "2026-10-12" }, "agreement": { "verdict": "unclear", "reasons": [ "Mouse: higher in PDAC in all three comparisons (log2FC 0.90 to 2.36, all adjusted p < 0.05).", "Human bulk (Xena): tumor median 459.2 TPM vs normal pancreas 92.2 TPM, log2 difference +2.32, p = 1.1e-55.", "No reviewed human study measured it inside cancer cells and found it higher." ], "note": "The human tumor vs normal evidence found here is bulk tissue proteomics, not measured inside cancer cells." } }, { "mouse": "Tpt1", "human": "TPT1", "human_name": "tumor protein, translationally-controlled 1", "orthology": { "mgi_id": "MGI:104890", "mouse_entrez": "22070", "hgnc_id": "HGNC:12022", "ensembl": "ENSG00000133112", "entrez": "7178", "location": "13q14.13", "hgnc_xref_agrees": true, "methods_matched": [ "Ensembl Compara", "HGNC", "Hieranoid", "InParanoid", "OMA", "OrthoFinder", "OrthoInspector", "PANTHER", "PhylomeDB", "SonicParanoid" ], "methods_not_matched": [], "other_stringent_human": [ { "symbol": "TPT1P8", "hgnc_id": "HGNC:24088", "best": "No", "best_reverse": "Yes", "n_methods": 4 } ] }, "mouse_result": { "A": { "gene": "Tpt1", "rank_up": 22, "log2fc": 1.541, "padj": 0.0, "pct_in": 1.0, "pct_ref": 0.999, "direction": "up in PDAC", "name": "K5-dominant tumor epithelial clusters (0,1,2,3,7) vs K4-dominant ADM cluster (4)" }, "B": { "gene": "Tpt1", "rank_up": 7, "log2fc": 1.011, "padj": 6.05e-157, "pct_in": 1.0, "pct_ref": 0.999, "direction": "up in PDAC", "name": "Classical ductal-like cluster 1 vs ADM cluster 4" }, "C": { "gene": "Tpt1", "rank_up": 10, "log2fc": 1.811, "padj": 0.0, "pct_in": 1.0, "pct_ref": 0.997, "direction": "up in PDAC", "name": "All K5 cells vs all K4 cells" } }, "xena": { "probe": "ENSG00000133112.16", "tumor": { "n": 178, "median_log2": 12.425, "q1_log2": 12.262, "q3_log2": 12.71, "median_tpm": 5499.2 }, "gtex_normal": { "n": 167, "median_log2": 11.42, "q1_log2": 11.16, "q3_log2": 11.7, "median_tpm": 2740.1 }, "tcga_adjacent_normal": { "n": 4, "median_log2": 12.41, "q1_log2": 12.272, "q3_log2": 12.51, "median_tpm": 5442.3 }, "log2_median_diff": 1.005, "mwu_p": 1.36e-51, "auc_tumor_gt_normal": 0.971 }, "hpa": { "rna_tissue_specificity": "Tissue enhanced", "rna_tissue_distribution": "Detected in all", "pancreas_ntpm": 10034.3, "duct_ncpm": 2920.8, "acinar_ncpm": 14447.7, "prog_tcga": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "4.15e-2" }, "prog_validation": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "8.41e-2" }, "page": "https://www.proteinatlas.org/ENSG00000133112-TPT1/cancer/pancreatic+cancer", "tissue_page": "https://www.proteinatlas.org/ENSG00000133112-TPT1/tissue", "url": "https://www.proteinatlas.org/api/search_download.php?search=ENSG00000133112&format=json&columns=g,eg,rnats,rnatd,t_RNA_pancreas,sc_RNA_Pancreatic_duct_cells,sc_RNA_Pancreatic_acinar_cells,prognostic_Pancreatic_Adenocarcinoma_(TCGA),prognostic_Pancreatic_Adenocarcinoma_(validation)&compress=no" }, "literature": { "papers": [ { "pmid": "28928875", "title": "MicroRNA-216b-5p Functions as a Tumor-suppressive RNA by Targeting TPT1 in Pancreatic Cancer Cells", "journal": "J Cancer", "year": "2017", "first_author": "You Y", "summary": "Reported TPT1 mRNA higher in pancreatic cancer tissue and identified it as a target of the tumor-suppressive microRNA miR-216b-5p; lowering TPT1 slowed cancer cells.", "cell_resolved_higher": false, "url": "https://pubmed.ncbi.nlm.nih.gov/28928875/" }, { "pmid": "32792860", "title": "MiR-216a-5p inhibits tumorigenesis in Pancreatic Cancer by targeting TPT1/mTORC1 and is mediated by LINC01133", "journal": "Int J Biol Sci", "year": "2020", "first_author": "Zhang J", "summary": "A second microRNA study (miR-216a-5p) that also targets TPT1; the work centres on the microRNA, with TPT1 as a downstream effector. An erratum was later published (PMID 35342339).", "cell_resolved_higher": false, "url": "https://pubmed.ncbi.nlm.nih.gov/32792860/" } ], "search_term": "(TPT1[tiab] OR TCTP[tiab]) AND (pancreatic cancer[tiab] OR pancreatic ductal adenocarcinoma[tiab] OR pancreatic adenocarcinoma[tiab] OR PDAC[tiab])", "search_count": 9, "search_retrieved": "2026-10-12" }, "agreement": { "verdict": "unclear", "reasons": [ "Mouse: higher in PDAC in all three comparisons (log2FC 1.01 to 1.81, all adjusted p < 0.05).", "Human bulk (Xena): tumor median 5499.2 TPM vs normal pancreas 2740.1 TPM, log2 difference +1.00, p = 1.4e-51.", "No reviewed human study measured it inside cancer cells and found it higher." ], "note": "Alliance also lists TPT1P8, a human pseudogene, as a weaker stringent match. TPT1 is the best-scoring ortholog in both directions." } }, { "mouse": "Aprt", "human": "APRT", "human_name": "adenine phosphoribosyltransferase", "orthology": { "mgi_id": "MGI:88061", "mouse_entrez": "11821", "hgnc_id": "HGNC:626", "ensembl": "ENSG00000198931", "entrez": "353", "location": "16q24.3", "hgnc_xref_agrees": true, "methods_matched": [ "Ensembl Compara", "HGNC", "Hieranoid", "InParanoid", "OMA", "OrthoFinder", "OrthoInspector", "PANTHER", "PhylomeDB", "SonicParanoid" ], "methods_not_matched": [], "other_stringent_human": [] }, "mouse_result": { "A": { "gene": "Aprt", "rank_up": 14, "log2fc": 2.589, "padj": 0.0, "pct_in": 0.974, "pct_ref": 0.698, "direction": "up in PDAC", "name": "K5-dominant tumor epithelial clusters (0,1,2,3,7) vs K4-dominant ADM cluster (4)" }, "B": { "gene": "Aprt", "rank_up": 177, "log2fc": 1.079, "padj": 2e-50, "pct_in": 0.92, "pct_ref": 0.698, "direction": "up in PDAC", "name": "Classical ductal-like cluster 1 vs ADM cluster 4" }, "C": { "gene": "Aprt", "rank_up": 13, "log2fc": 2.841, "padj": 0.0, "pct_in": 0.969, "pct_ref": 0.628, "direction": "up in PDAC", "name": "All K5 cells vs all K4 cells" } }, "xena": { "probe": "ENSG00000198931.10", "tumor": { "n": 178, "median_log2": 7.242, "q1_log2": 6.905, "q3_log2": 7.576, "median_tpm": 151.4 }, "gtex_normal": { "n": 167, "median_log2": 6.075, "q1_log2": 5.736, "q3_log2": 6.353, "median_tpm": 67.4 }, "tcga_adjacent_normal": { "n": 4, "median_log2": 6.978, "q1_log2": 6.681, "q3_log2": 7.226, "median_tpm": 126.1 }, "log2_median_diff": 1.167, "mwu_p": 9.24e-44, "auc_tumor_gt_normal": 0.932 }, "hpa": { "rna_tissue_specificity": "Low tissue specificity", "rna_tissue_distribution": "Detected in all", "pancreas_ntpm": 165.3, "duct_ncpm": 128.4, "acinar_ncpm": 262.9, "prog_tcga": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "9.14e-3" }, "prog_validation": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "1.47e-1" }, "page": "https://www.proteinatlas.org/ENSG00000198931-APRT/cancer/pancreatic+cancer", "tissue_page": "https://www.proteinatlas.org/ENSG00000198931-APRT/tissue", "url": "https://www.proteinatlas.org/api/search_download.php?search=ENSG00000198931&format=json&columns=g,eg,rnats,rnatd,t_RNA_pancreas,sc_RNA_Pancreatic_duct_cells,sc_RNA_Pancreatic_acinar_cells,prognostic_Pancreatic_Adenocarcinoma_(TCGA),prognostic_Pancreatic_Adenocarcinoma_(validation)&compress=no" }, "literature": { "papers": [], "search_term": "(APRT[tiab] OR \"adenine phosphoribosyltransferase\"[tiab]) AND (pancreatic cancer[tiab] OR pancreatic ductal adenocarcinoma[tiab] OR pancreatic adenocarcinoma[tiab] OR PDAC[tiab])", "search_count": 1, "search_retrieved": "2026-10-12" }, "agreement": { "verdict": "unclear", "reasons": [ "Mouse: higher in PDAC in all three comparisons (log2FC 1.08 to 2.84, all adjusted p < 0.05).", "Human bulk (Xena): tumor median 151.4 TPM vs normal pancreas 67.4 TPM, log2 difference +1.17, p = 9.2e-44.", "No reviewed human study measured it inside cancer cells and found it higher (no pancreatic cancer paper found)." ], "note": "The PubMed search returned one paper, about a drug strategy in which APRT activates adenine-analog prodrugs. It does not measure APRT in pancreatic cancer, so it is not listed." } }, { "mouse": "Tm4sf1", "human": "TM4SF1", "human_name": "transmembrane 4 L six family member 1", "orthology": { "mgi_id": "MGI:104678", "mouse_entrez": "17112", "hgnc_id": "HGNC:11853", "ensembl": "ENSG00000169908", "entrez": "4071", "location": "3q25.1", "hgnc_xref_agrees": true, "methods_matched": [ "Ensembl Compara", "HGNC", "Hieranoid", "InParanoid", "OMA", "OrthoFinder", "OrthoInspector", "PANTHER", "PhylomeDB", "SonicParanoid" ], "methods_not_matched": [], "other_stringent_human": [] }, "mouse_result": { "A": { "gene": "Tm4sf1", "rank_up": 9, "log2fc": 5.854, "padj": 0.0, "pct_in": 0.897, "pct_ref": 0.096, "direction": "up in PDAC", "name": "K5-dominant tumor epithelial clusters (0,1,2,3,7) vs K4-dominant ADM cluster (4)" }, "B": { "gene": "Tm4sf1", "rank_up": 87, "log2fc": 2.429, "padj": 2.16e-75, "pct_in": 0.508, "pct_ref": 0.096, "direction": "up in PDAC", "name": "Classical ductal-like cluster 1 vs ADM cluster 4" }, "C": { "gene": "Tm4sf1", "rank_up": 7, "log2fc": 6.304, "padj": 0.0, "pct_in": 0.892, "pct_ref": 0.066, "direction": "up in PDAC", "name": "All K5 cells vs all K4 cells" } }, "xena": { "probe": "ENSG00000169908.10", "tumor": { "n": 178, "median_log2": 8.503, "q1_log2": 7.753, "q3_log2": 9.188, "median_tpm": 362.7 }, "gtex_normal": { "n": 167, "median_log2": 5.119, "q1_log2": 4.444, "q3_log2": 5.94, "median_tpm": 34.8 }, "tcga_adjacent_normal": { "n": 4, "median_log2": 8.203, "q1_log2": 7.489, "q3_log2": 8.421, "median_tpm": 294.6 }, "log2_median_diff": 3.384, "mwu_p": 2.96e-45, "auc_tumor_gt_normal": 0.94 }, "hpa": { "rna_tissue_specificity": "Low tissue specificity", "rna_tissue_distribution": "Detected in all", "pancreas_ntpm": 199.8, "duct_ncpm": 1483.6, "acinar_ncpm": 7870.8, "prog_tcga": { "is_prognostic": true, "label": "potential prognostic", "type": "unfavorable", "p": "7.66e-4" }, "prog_validation": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "1.95e-3" }, "page": "https://www.proteinatlas.org/ENSG00000169908-TM4SF1/cancer/pancreatic+cancer", "tissue_page": "https://www.proteinatlas.org/ENSG00000169908-TM4SF1/tissue", "url": "https://www.proteinatlas.org/api/search_download.php?search=ENSG00000169908&format=json&columns=g,eg,rnats,rnatd,t_RNA_pancreas,sc_RNA_Pancreatic_duct_cells,sc_RNA_Pancreatic_acinar_cells,prognostic_Pancreatic_Adenocarcinoma_(TCGA),prognostic_Pancreatic_Adenocarcinoma_(validation)&compress=no" }, "literature": { "papers": [ { "pmid": "27459514", "title": "TM4SF1 Regulates Pancreatic Cancer Migration and Invasion In Vitro and In Vivo", "journal": "Cell Physiol Biochem", "year": "2016", "first_author": "Cao J", "summary": "TM4SF1 was higher in pancreatic cancer than in adjacent tissue by qPCR and immunostaining; silencing it reduced invasion and metastasis in mouse models.", "cell_resolved_higher": true, "url": "https://pubmed.ncbi.nlm.nih.gov/27459514/" }, { "pmid": "26035794", "title": "TM4SF1 as a prognostic marker of pancreatic ductal adenocarcinoma is involved in migration and invasion of cancer cells", "journal": "Int J Oncol", "year": "2015", "first_author": "Zheng B", "summary": "Immunostaining found TM4SF1 in cancer cells, but here patients with higher TM4SF1 lived longer. This runs against the HPA prognostic call below.", "cell_resolved_higher": false, "url": "https://pubmed.ncbi.nlm.nih.gov/26035794/" } ], "search_term": "TM4SF1[tiab] AND (pancreatic cancer[tiab] OR pancreatic ductal adenocarcinoma[tiab] OR pancreatic adenocarcinoma[tiab] OR PDAC[tiab])", "search_count": 8, "search_retrieved": "2026-10-12" }, "agreement": { "verdict": "agree", "reasons": [ "Mouse: higher in PDAC in all three comparisons (log2FC 2.43 to 6.30, all adjusted p < 0.05).", "Human bulk (Xena): tumor median 362.7 TPM vs normal pancreas 34.8 TPM, log2 difference +3.38, p = 3e-45.", "Cell-level human evidence of higher expression in cancer cells: PMID 27459514." ], "note": "Expression direction agrees, but the survival evidence conflicts: HPA calls high TM4SF1 unfavorable in TCGA PAAD, while a 2015 immunostaining study found longer survival with high TM4SF1." } }, { "mouse": "Gapdh", "human": "GAPDH", "human_name": "glyceraldehyde-3-phosphate dehydrogenase", "orthology": { "mgi_id": "MGI:95640", "mouse_entrez": "14433", "hgnc_id": "HGNC:4141", "ensembl": "ENSG00000111640", "entrez": "2597", "location": "12p13.31", "hgnc_xref_agrees": true, "methods_matched": [ "Ensembl Compara", "HGNC", "Hieranoid", "InParanoid", "OMA", "OrthoFinder", "OrthoInspector", "PANTHER", "PhylomeDB", "SonicParanoid" ], "methods_not_matched": [], "other_stringent_human": [] }, "mouse_result": { "A": { "gene": "Gapdh", "rank_up": 2, "log2fc": 2.766, "padj": 0.0, "pct_in": 0.999, "pct_ref": 0.98, "direction": "up in PDAC", "name": "K5-dominant tumor epithelial clusters (0,1,2,3,7) vs K4-dominant ADM cluster (4)" }, "B": { "gene": "Gapdh", "rank_up": 2, "log2fc": 1.615, "padj": 8.49e-210, "pct_in": 0.996, "pct_ref": 0.98, "direction": "up in PDAC", "name": "Classical ductal-like cluster 1 vs ADM cluster 4" }, "C": { "gene": "Gapdh", "rank_up": 1, "log2fc": 2.983, "padj": 0.0, "pct_in": 0.999, "pct_ref": 0.946, "direction": "up in PDAC", "name": "All K5 cells vs all K4 cells" } }, "xena": { "probe": "ENSG00000111640.14", "tumor": { "n": 178, "median_log2": 11.24, "q1_log2": 10.845, "q3_log2": 11.638, "median_tpm": 2418.7 }, "gtex_normal": { "n": 167, "median_log2": 7.851, "q1_log2": 7.478, "q3_log2": 8.186, "median_tpm": 230.9 }, "tcga_adjacent_normal": { "n": 4, "median_log2": 10.665, "q1_log2": 10.275, "q3_log2": 10.91, "median_tpm": 1623.6 }, "log2_median_diff": 3.389, "mwu_p": 2.31e-57, "auc_tumor_gt_normal": 0.997 }, "hpa": { "rna_tissue_specificity": "Group enriched", "rna_tissue_distribution": "Detected in all", "pancreas_ntpm": 602.3, "duct_ncpm": 1339.8, "acinar_ncpm": 1438.5, "prog_tcga": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "4.63e-3" }, "prog_validation": { "is_prognostic": false, "label": "unprognostic", "type": "", "p": "4.52e-2" }, "page": "https://www.proteinatlas.org/ENSG00000111640-GAPDH/cancer/pancreatic+cancer", "tissue_page": "https://www.proteinatlas.org/ENSG00000111640-GAPDH/tissue", "url": "https://www.proteinatlas.org/api/search_download.php?search=ENSG00000111640&format=json&columns=g,eg,rnats,rnatd,t_RNA_pancreas,sc_RNA_Pancreatic_duct_cells,sc_RNA_Pancreatic_acinar_cells,prognostic_Pancreatic_Adenocarcinoma_(TCGA),prognostic_Pancreatic_Adenocarcinoma_(validation)&compress=no" }, "literature": { "papers": [ { "pmid": "17332923", "title": "Expression of glycolytic enzymes is increased in pancreatic cancerous tissues as evidenced by proteomic profiling by two-dimensional electrophoresis and liquid chromatography-mass spectrometry/mass spectrometry", "journal": "Int J Oncol", "year": "2007", "first_author": "Mikuriya K", "summary": "Same proteomics study as TPI1: GAPDH appeared among the glycolysis proteins raised in tumor vs paired non-cancerous tissue.", "cell_resolved_higher": false, "url": "https://pubmed.ncbi.nlm.nih.gov/17332923/" }, { "pmid": "30296496", "title": "Mutant p53 prevents GAPDH nuclear translocation in pancreatic cancer cells favoring glycolysis and 2-deoxyglucose sensitivity", "journal": "Biochim Biophys Acta Mol Cell Res", "year": "2018", "first_author": "Butera G", "summary": "In PDAC cell lines, mutant p53 kept GAPDH in the cytoplasm, which supported glycolysis and cell survival. A mechanism paper, not a tumor vs normal comparison.", "cell_resolved_higher": false, "url": "https://pubmed.ncbi.nlm.nih.gov/30296496/" } ], "search_term": "GAPDH[ti] AND (pancreatic cancer[tiab] OR pancreatic ductal adenocarcinoma[tiab] OR pancreatic adenocarcinoma[tiab] OR PDAC[tiab])", "search_count": 5, "search_retrieved": "2026-10-12" }, "agreement": { "verdict": "unclear", "reasons": [ "Mouse: higher in PDAC in all three comparisons (log2FC 1.61 to 2.98, all adjusted p < 0.05).", "Human bulk (Xena): tumor median 2418.7 TPM vs normal pancreas 230.9 TPM, log2 difference +3.39, p = 2.3e-57.", "No reviewed human study measured it inside cancer cells and found it higher." ], "note": "GAPDH is widely used as a housekeeping (reference) gene. A shift in GAPDH is real data but is often read as a change in glycolysis or cell state rather than a specific cancer marker." } } ], "summary": { "agree": 5, "disagree": 0, "unclear": 5 }, "rule": { "agree": "Human bulk tumor is higher than normal pancreas (log2 median difference of at least 1, p < 0.05) and at least one reviewed human study measured the gene inside cancer cells and found it higher than in non-malignant cells.", "disagree": "Human bulk tumor is lower than normal pancreas (log2 difference of -1 or less, p < 0.05).", "unclear": "Anything else: the bulk signal is small, or no reviewed study places the increase in the cancer cells themselves.", "not_used": "HPA survival (prognostic) calls are shown but do not decide the verdict, because her result is about expression level, not survival." }, "provenance": { "built": "2026-10-11 (America/Los_Angeles); API retrieval dates below are UTC", "mouse": { "file": "/clusterscope/real-data.json", "page": "/clusterscope#real", "source": "Burdziak et al., Science 2023, PMID 37167403, GEO GSE207938 (GSE207938_ProgressionCohort.h5ad)", "n_cells_total": 6618, "n_genes_tested": 16357, "n_k4": 1254, "n_k5": 5364, "samples": { "K4": [ "DAC_C301-EPI_1", "DAC_C301-EPI_2" ], "K5": [ "DAC_D020_p5_Epi", "Ag-PDAC-PT-Kate", "DACC963PT_Kate_plus" ] }, "de": "Wilcoxon rank-sum (scanpy, tie-corrected), Benjamini-Hochberg; log2FC from scanpy", "versions": { "scanpy": "1.12.4" }, "date": "2026-10-11", "note": "Python/scanpy reanalysis of the public dataset, not Ridhi's original R/Seurat code." }, "orthology": { "alliance": { "url": "https://www.alliancegenome.org/api/gene//orthologs?filter.stringency=stringent", "release": "9.1.0", "release_date": "2026-09-02", "retrieved": "2026-10-12" }, "mygene": { "url": "https://mygene.info/v3/query?q=symbol:&species=mouse", "build": "20260922", "retrieved": "2026-10-12" }, "hgnc": { "url": "https://rest.genenames.org/fetch/hgnc_id/", "retrieved": "2026-10-12" } }, "xena": { "hub": "https://toil.xenahubs.net", "api": "https://toil.xenahubs.net/data/", "expression_dataset": "TcgaTargetGtex_rsem_gene_tpm", "expression_version": "2016-09-03", "unit": "log2(tpm+0.001)", "pipeline": "UCSC TOIL RNA-seq recompute", "probemap": "probeMap/gencode.v23.annotation.gene.probemap", "phenotype_dataset": "TcgaTargetGTEX_phenotype.txt", "phenotype_version": "2016-09-15", "retrieved": "2026-10-12", "browser_url": "https://xenabrowser.net/datapages/?dataset=TcgaTargetGtex_rsem_gene_tpm&host=https%3A%2F%2Ftoil.xenahubs.net", "groups": { "tumor": "TCGA, detailed_category = Pancreatic Adenocarcinoma, _sample_type = Primary Tumor", "normal": "GTEx, _primary_site = Pancreas", "tcga_adjacent_normal": "TCGA PAAD Solid Tissue Normal (shown for context only)" }, "n_tumor": 178, "n_gtex": 167, "n_tcga_normal": 4, "test": "two-sided Mann-Whitney U on log2(TPM+0.001), scipy 1.18.0" }, "hpa": { "version": "25.1", "release_date": "2026-05-25", "ensembl": "109", "api": "https://www.proteinatlas.org/api/search_download.php", "columns": [ "g", "eg", "rnats", "rnatd", "t_RNA_pancreas", "sc_RNA_Pancreatic_duct_cells", "sc_RNA_Pancreatic_acinar_cells", "prognostic_Pancreatic_Adenocarcinoma_(TCGA)", "prognostic_Pancreatic_Adenocarcinoma_(validation)" ], "retrieved": "2026-10-12", "prognostic_rule": "HPA calls a gene prognostic in a cohort when the log-rank p value is below 0.001; otherwise it is listed as unprognostic even if p is below 0.05." }, "pubmed": { "api": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ (esearch, efetch, esummary)", "retrieved": "2026-10-12" }, "gepia": { "used": false, "why": "GEPIA2 has no documented, stable public API I could verify, and its tumor vs normal values come from the same TCGA and GTEx data as the UCSC Xena Toil recompute used here." } } }