KnockTF 2.0: a Comprehensive Gene Expression Profile Database with Knockdown/knockout of Transcription (co-)factors in Multiple Species

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2023 Nov 13

PMID 37956336

Authors

Chenchen Feng

Chao Song

Shuang Song

Guorui Zhang

Mingxue Yin

Yuexin Zhang

Fengcui Qian

Qiuyu Wang

Maozu Guo

Chunquan Li

Affiliations

Soon will be listed here.

Abstract

Transcription factors (TFs), transcription co-factors (TcoFs) and their target genes perform essential functions in diseases and biological processes. KnockTF 2.0 (http://www.licpathway.net/KnockTF/index.html) aims to provide comprehensive gene expression profile datasets before/after T(co)F knockdown/knockout across multiple tissue/cell types of different species. Compared with KnockTF 1.0, KnockTF 2.0 has the following improvements: (i) Newly added T(co)F knockdown/knockout datasets in mice, Arabidopsis thaliana and Zea mays and also an expanded scale of datasets in humans. Currently, KnockTF 2.0 stores 1468 manually curated RNA-seq and microarray datasets associated with 612 TFs and 172 TcoFs disrupted by different knockdown/knockout techniques, which are 2.5 times larger than those of KnockTF 1.0. (ii) Newly added (epi)genetic annotations for T(co)F target genes in humans and mice, such as super-enhancers, common SNPs, methylation sites and chromatin interactions. (iii) Newly embedded and updated search and analysis tools, including T(co)F Enrichment (GSEA), Pathway Downstream Analysis and Search by Target Gene (BLAST). KnockTF 2.0 is a comprehensive update of KnockTF 1.0, which provides more T(co)F knockdown/knockout datasets and (epi)genetic annotations across multiple species than KnockTF 1.0. KnockTF 2.0 facilitates not only the identification of functional T(co)Fs and target genes but also the investigation of their roles in the physiological and pathological processes.

Citing Articles

TFTF: An R-Based Integrative Tool for Decoding Human Transcription Factor-Target Interactions.

Wang J Biomolecules. 2024; 14(7).

PMID: 39062464 PMC: 11274450. DOI: 10.3390/biom14070749.

The Prognostic and Therapeutic Potential of Fragile X Mental Retardation 1 () Gene Expression in Prostate Adenocarcinoma: Insights into Survival Outcomes and Oncogenic Pathway Modulation.

Baldi S, Amer B, Alnadari F, Al-Mogahed M, Gao Y, Gamallat Y Int J Mol Sci. 2024; 25(13).

PMID: 39000397 PMC: 11242135. DOI: 10.3390/ijms25137290.

Comprehensive analysis of the clinical significance and molecular mechanism of T-box transcription factor 3 in osteosarcoma.

Man Y, Xu H, Chen P, Sun Y, He M J Cancer. 2024; 15(12):4007-4019.

PMID: 38911382 PMC: 11190752. DOI: 10.7150/jca.96168.

Recent advances in exploring transcriptional regulatory landscape of crops.

Huo Q, Song R, Ma Z Front Plant Sci. 2024; 15:1421503.

PMID: 38903438 PMC: 11188431. DOI: 10.3389/fpls.2024.1421503.

References

Sherry S, Ward M, Kholodov M, Baker J, Phan L, Smigielski E . dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2000; 29(1):308-11. PMC: 29783. DOI: 10.1093/nar/29.1.308. View

Wang L, Zhang W, Li C, Chen X, Huang J . Identification of biomarkers related to copper metabolism in patients with pulmonary arterial hypertension. BMC Pulm Med. 2023; 23(1):31. PMC: 9868507. DOI: 10.1186/s12890-023-02326-6. View

Gamazon E, Zhang W, Konkashbaev A, Duan S, Kistner E, Nicolae D . SCAN: SNP and copy number annotation. Bioinformatics. 2009; 26(2):259-62. PMC: 2852202. DOI: 10.1093/bioinformatics/btp644. View

Salazar M, Ratnam M, Patki M, Kisovic I, Trumbly R, Iman M . During hormone depletion or tamoxifen treatment of breast cancer cells the estrogen receptor apoprotein supports cell cycling through the retinoic acid receptor α1 apoprotein. Breast Cancer Res. 2011; 13(1):R18. PMC: 3109587. DOI: 10.1186/bcr2827. View

Vaquerizas J, Kummerfeld S, Teichmann S, Luscombe N . A census of human transcription factors: function, expression and evolution. Nat Rev Genet. 2009; 10(4):252-63. DOI: 10.1038/nrg2538. View

Lee T, Young R . Transcriptional regulation and its misregulation in disease. Cell. 2013; 152(6):1237-51. PMC: 3640494. DOI: 10.1016/j.cell.2013.02.014. View

Wang F, Bai X, Wang Y, Jiang Y, Ai B, Zhang Y . ATACdb: a comprehensive human chromatin accessibility database. Nucleic Acids Res. 2020; 49(D1):D55-D64. PMC: 7779059. DOI: 10.1093/nar/gkaa943. View

Xia K, Shabalin A, Huang S, Madar V, Zhou Y, Wang W . seeQTL: a searchable database for human eQTLs. Bioinformatics. 2011; 28(3):451-2. PMC: 3268245. DOI: 10.1093/bioinformatics/btr678. View

Cunningham T, Duester G . Mechanisms of retinoic acid signalling and its roles in organ and limb development. Nat Rev Mol Cell Biol. 2015; 16(2):110-23. PMC: 4636111. DOI: 10.1038/nrm3932. View

10.

Gill G . Regulation of the initiation of eukaryotic transcription. Essays Biochem. 2002; 37:33-43. DOI: 10.1042/bse0370033. View

11.

Chandarlapaty S, Chen D, He W, Sung P, Samoila A, You D . Prevalence of ESR1 Mutations in Cell-Free DNA and Outcomes in Metastatic Breast Cancer: A Secondary Analysis of the BOLERO-2 Clinical Trial. JAMA Oncol. 2016; 2(10):1310-1315. PMC: 5063698. DOI: 10.1001/jamaoncol.2016.1279. View

12.

Haeussler M, Schonig K, Eckert H, Eschstruth A, Mianne J, Renaud J . Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016; 17(1):148. PMC: 4934014. DOI: 10.1186/s13059-016-1012-2. View

13.

Abecasis G, Auton A, Brooks L, DePristo M, Durbin R, Handsaker R . An integrated map of genetic variation from 1,092 human genomes. Nature. 2012; 491(7422):56-65. PMC: 3498066. DOI: 10.1038/nature11632. View

14.

Li M, Liu Z, Wang P, Wong M, Nelson M, Kocher J . GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res. 2015; 44(D1):D869-76. PMC: 4702921. DOI: 10.1093/nar/gkv1317. View

15.

Schmeier S, Alam T, Essack M, Bajic V . TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. Nucleic Acids Res. 2016; 45(D1):D145-D150. PMC: 5210517. DOI: 10.1093/nar/gkw1007. View

16.

Robasky K, Bulyk M . UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res. 2010; 39(Database issue):D124-8. PMC: 3013812. DOI: 10.1093/nar/gkq992. View

17.

Grant C, Bailey T, Noble W . FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011; 27(7):1017-8. PMC: 3065696. DOI: 10.1093/bioinformatics/btr064. View

18.

Zhang X, Emerald B, Mukhina S, Mohankumar K, Kraemer A, Yap A . HOXA1 is required for E-cadherin-dependent anchorage-independent survival of human mammary carcinoma cells. J Biol Chem. 2005; 281(10):6471-81. DOI: 10.1074/jbc.M512666200. View

19.

Zabidi M, Stark A . Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors. Trends Genet. 2016; 32(12):801-814. PMC: 6795546. DOI: 10.1016/j.tig.2016.10.003. View

20.

Dustin D, Gu G, Fuqua S . ESR1 mutations in breast cancer. Cancer. 2019; 125(21):3714-3728. PMC: 6788940. DOI: 10.1002/cncr.32345. View