ZKSCAN1 Gene

HGNC Family	Zinc fingers
Name	zinc finger with KRAB and SCAN domains 1
Description	This gene encodes a member of the Kruppel C2H2-type zinc-finger family of proteins. This encoded protein may function as a transcription factor that regulates the expression of GABA type-A receptors in the brain. Transcripts from this gene have been shown to form stable and abundant circular RNAs. Elevated expression of this gene has been observed in gastric cancer and the encoded protein may stimulate migration and invasion of human gastric cancer cells. [provided by RefSeq, Oct 2016]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nIn hepatocellular carcinoma (HCC), the ZKSCAN1 gene is expressed as both a conventional linear mRNA and a circular RNA (circZKSCAN1) with distinct yet cooperative tumor‐suppressive functions. The linear form primarily influences cellular metabolism, whereas circZKSCAN1 modulates several cancer‐related signaling pathways. In particular, reduced levels of these transcripts correlate with unfavorable clinicopathological features such as larger tumor size, increased tumor nodularity, vascular invasion, and higher tumor grade. Mechanistically, circZKSCAN1 has been shown to regulate cancer stemness by competitively binding to RNA‐binding proteins (e.g., FMRP) to attenuate the transcriptional activity of the Wnt pathway, and recent studies further suggest that circZKSCAN1 can encode a secretory peptide (circZKSaa) that may contribute to its anti‐tumor effects."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "5"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn contrast to the tumor‐suppressive role of ZKSCAN1 in liver cancer, several studies have investigated a related zinc finger family member, ZNF139, in the context of gastric cancer. ZNF139 is frequently overexpressed in gastric cancer tissues and cell lines, and its upregulation is associated with enhanced invasive and migratory capacities, as well as multi‐drug resistance. Functionally, ZNF139 appears to promote the expression of drug resistance and anti‐apoptotic genes (such as MDR1/P-gp, MRP1, and Bcl-2) while suppressing pro-apoptotic factors (e.g., Bax). Moreover, microRNAs such as miR-195-5p and miR-185 have been identified as negative regulators of ZNF139, and their suppression exacerbates drug resistance. Collectively, these findings highlight the divergent roles of these zinc finger proteins in cancer, with ZKSCAN1 acting as a tumor suppressor in HCC—through regulation of metabolic and signaling pathways—and ZNF139 functioning as an oncogenic driver in gastric cancer by fostering cell survival, metastasis, and chemoresistance."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "6", "end_ref": "12"}]}, {"type": "t", "text": ""}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Zhicheng Yao, Jingyan Luo, Kunpeng Hu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "ZKSCAN1 gene and its related circular RNA (circZKSCAN1) both inhibit hepatocellular carcinoma cell growth, migration, and invasion but through different signaling pathways."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Oncol (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/1878-0261.12045"}], "href": "https://doi.org/10.1002/1878-0261.12045"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28211215"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28211215"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Yan-Jing Zhu, Bo Zheng, Gui-Juan Luo, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Circular RNAs negatively regulate cancer stem cells by physically binding FMRP against CCAR1 complex in hepatocellular carcinoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Theranostics (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.7150/thno.32796"}], "href": "https://doi.org/10.7150/thno.32796"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31281495"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31281495"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Junming Bi, Hongwei Liu, Wei Dong, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Circular RNA circ-ZKSCAN1 inhibits bladder cancer progression through miR-1178-3p/p21 axis and acts as a prognostic factor of recurrence."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cancer (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s12943-019-1060-9"}], "href": "https://doi.org/10.1186/s12943-019-1060-9"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31481066"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31481066"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Jing Li, Siyang Bao, Linqi Wang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CircZKSCAN1 Suppresses Hepatocellular Carcinoma Tumorigenesis by Regulating miR-873-5p/Downregulation of Deleted in Liver Cancer 1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Dig Dis Sci (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s10620-020-06789-z"}], "href": "https://doi.org/10.1007/s10620-020-06789-z"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33439397"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33439397"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Runjie Song, Shuoqian Ma, Jiajia Xu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A novel polypeptide encoded by the circular RNA ZKSCAN1 suppresses HCC via degradation of mTOR."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cancer (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s12943-023-01719-9"}], "href": "https://doi.org/10.1186/s12943-023-01719-9"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36691031"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36691031"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Yong Li, Bi-bo Tan, Qun Zhao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Regulatory mechanism of ZNF139 in multi-drug resistance of gastric cancer cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Biol Rep (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s11033-014-3224-4"}], "href": "https://doi.org/10.1007/s11033-014-3224-4"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24515389"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24515389"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Y Li, B B Tan, Q Zhao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "ZNF139 promotes tumor metastasis by increasing migration and invasion in human gastric cancer cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Neoplasma (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.4149/neo_2014_037"}], "href": "https://doi.org/10.4149/neo_2014_037"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24824930"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24824930"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Li-qiao Fan, Yong Li, Qun Zhao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Comparative proteomics in gastric cancer cell line BGC823 after ZNF139 gene inhibited with RNA interference."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hepatogastroenterology (2014)"}]}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25436386"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25436386"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Yong Li, Qun Zhao, Li-Qiao Fan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Zinc finger protein 139 expression in gastric cancer and its clinical significance."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "World J Gastroenterol (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.3748/wjg.v20.i48.18346"}], "href": "https://doi.org/10.3748/wjg.v20.i48.18346"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25561801"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25561801"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Liqiao Fan, Bibo Tan, Yong Li, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Silencing of ZNF139-siRNA induces apoptosis in human gastric cancer cell line BGC823."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Int J Clin Exp Pathol (2015)"}]}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26722429"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26722429"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Hongfeng Nie, Jixing Mu, Jinsheng Wang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "miR‑195‑5p regulates multi‑drug resistance of gastric cancer cells via targeting ZNF139."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Oncol Rep (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.3892/or.2018.6524"}], "href": "https://doi.org/10.3892/or.2018.6524"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29956811"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29956811"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Bibo Tan, Yong Li, Qun Zhao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "ZNF139 increases multidrug resistance in gastric cancer cells by inhibiting "}, {"type": "a", "children": [{"type": "t", "text": "i"}], "href": "i"}, {"type": "t", "text": "miR-185"}, {"type": "a", "children": [{"type": "t", "text": "/i"}], "href": "/i"}, {"type": "t", "text": "."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biosci Rep (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1042/BSR20181023"}], "href": "https://doi.org/10.1042/BSR20181023"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30126848"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30126848"}]}]}]}
Synonyms	PHZ-37, 9130423L19RIK, ZNF36, ZSCAN33, ZNF139, KOX18
Proteins	ZKSC1_HUMAN
NCBI Gene ID	7586
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

ZKSCAN1 has 6,283 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 107 datasets.

Click the + buttons to view associations for ZKSCAN1 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

ZKSCAN1 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by ZKSCAN1 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of ZKSCAN1 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of ZKSCAN1 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of ZKSCAN1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of ZKSCAN1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of ZKSCAN1 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of ZKSCAN1 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of ZKSCAN1 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of ZKSCAN1 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of ZKSCAN1 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of ZKSCAN1 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with ZKSCAN1 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with ZKSCAN1 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of ZKSCAN1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of ZKSCAN1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of ZKSCAN1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of ZKSCAN1 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing ZKSCAN1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing ZKSCAN1 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing ZKSCAN1 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with ZKSCAN1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with ZKSCAN1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of ZKSCAN1 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with ZKSCAN1 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with ZKSCAN1 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with ZKSCAN1 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of ZKSCAN1 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by ZKSCAN1 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with ZKSCAN1 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with ZKSCAN1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with ZKSCAN1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with ZKSCAN1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with ZKSCAN1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at ZKSCAN1 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of ZKSCAN1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of ZKSCAN1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing ZKSCAN1 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of ZKSCAN1 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with ZKSCAN1 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing ZKSCAN1 from the GeneSigDB Published Gene Signatures dataset.