TRRUST: a reference database of human transcriptional regulatory interactions

Han, Heonjong; Shim, Hongseok; Shin, Donghyun; Shim, Jung Eun; Ko, Yun-Hee; Shin, Junha; Kim, Hanhae; Cho, Ara; Kim, Eiru; Lee, Tak H.; Kim, Hyojin; Kim, Kyung-Soo; Yang, Sunmo; Bae, Dasom; Yun, Ayoung; Kim, Sunphil; Kim, Chan Yeong; Cho, Hyeon Jin; Kang, Byung Ha; Shin, Seunghwan; Lee, Insuk

doi:10.1038/srep11432

Cited by 345 publications

(305 citation statements)

References 37 publications

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“…To detect TF gene targets, the TRRUST database (transcriptional regulatory relationships unraveled by sentence-based text mining) (Han et al, 2015) was used, which contains 8015 interactions between 748 TF genes and 1975 non-TF genes. The interaction network between TFs with their gene target was constructed using the Cytoscape plug-in, GeneMANIA (Montojo et al, 2010).…”

Section: Gene Expression Profilingmentioning

confidence: 99%

Toward a Reference Gene Catalog of Human Primary Monocytes

Mirsafian

Ripen

Manaharan

et al. 2016

OMICS: A Journal of Integrative Biology

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Transcriptome analyses based on high-throughput RNA sequencing (RNA-Seq) provide powerful and quantitative characterization of cell types and in-depth understanding of biological systems in health and disease. In this study, we present a comprehensive transcriptome profile of human primary monocytes, a crucial component of the innate immune system. We performed deep RNA-Seq of monocytes from six healthy subjects and integrated our data with 10 other publicly available RNA-Seq datasets of human monocytes. A total of 1.9 billion reads were generated, which allowed us to capture most of the genes transcribed in human monocytes, including 11,994 protein-coding genes, 5558 noncoding genes (including long noncoding RNAs, precursor miRNAs, and others), 2819 pseudogenes, and 7034 putative novel transcripts. In addition, we profiled the expression pattern of 1155 transcription factors (TFs) in human monocytes, which are the main molecules in controlling the gene transcription. An interaction network was constructed among the top expressed TFs and their targeted genes, which revealed the potential key regulatory genes in biological function of human monocytes. The gene catalog of human primary monocytes provided in this study offers significant promise and future potential clinical applications in the fields of precision medicine, systems diagnostics, immunogenomics, and the development of innovative biomarkers and therapeutic monitoring strategies.

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Section: Gene Expression Profilingmentioning

confidence: 99%

Toward a Reference Gene Catalog of Human Primary Monocytes

Mirsafian

Ripen

Manaharan

et al. 2016

OMICS: A Journal of Integrative Biology

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“…Transcriptional Regulatory Network (TRN) We collect transcription factor (TF) -target gene (TG) interactions from the TRRUST database [25]. This dataset contains a total of 6, 314 regulatory interactions between 651 TFs and 2, 102 TGs.…”

Section: Cc-by 40 International License Peer-reviewed) Is the Authormentioning

confidence: 99%

Take ACTION to characterize the functional identity of single cells

Mohammadi

Ravindra

Gleich

et al. 2016

Preprint

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Single-cell transcriptomic data has the potential to radically redefine our view of cell type identity. Cells that were previously believed to be homogeneous are now clearly distinguishable in terms of their expression phenotype. Methods for automatically characterizing the functional identity of cells, and their associated properties, can be used to uncover processes involved in lineage differentiation as well as sub-typing cancer cells. They can also be used to suggest personalized therapies based on molecular signatures associated with pathology. We develop a new method, called ACTION, to infer the functional identity of cells from their transcriptional profile, classify them based on their dominant function, and reconstruct regulatory networks that are responsible for mediating their identity. Using ACTION, we identify novel Melanoma sub-types with differential survival rates and therapeutic responses, for which we provide biomarkers along with their underlying regulatory networks.

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“…Experimentally validated human transcription factors (TFs) and their target genes are collected from multiple databases: TRED [36], Neph2012 [37], ENCODE [38], Marbach2016 [39] and TRRUST [40]. Overall, 919 transcription factors are retrieved.…”

Section: Transcription Factor and Pathway Databasesmentioning

confidence: 99%

Transcription regulation by DNA methylation under stressful conditions in human cancer

Cao

Zhou

et al. 2017

Quant. Biol.

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Background: We aim to address one question: do cancer vs. normal tissue cells execute their transcription regulation essentially the same or differently, and why? Methods: We utilized an integrated computational study of cancer epigenomes and transcriptomes of 10 cancer types, by using penalized linear regression models to evaluate the regulatory effects of DNA methylations on gene expressions. Results: Our main discoveries are: (i) 56 genes have their expressions consistently regulated by DNA methylation specifically in cancer, which enrich pathways associated with micro-environmental stresses and responses, particularly oxidative stress; (ii) the level of involvement by DNA methylation in transcription regulation increases as a cancer advances for majority of the cancer types examined; (iii) transcription regulation in cancer vs. control tissue cells are substantially different, with the former being largely done through direct DNA methylation and the latter mainly done via transcriptional factors; (iv) the altered DNA methylation landscapes in cancer vs. control are predominantly accomplished by DNMT1, TET3 and CBX2, which are predicted to be the result of persistent stresses present in the intracellular and micro-environments of cancer cells, which is consistent with the general understanding about epigenomic functions. Conclusions: Our integrative analyses discovered that a large class of genes is regulated via direct DNA methylation of the genes in cancer, comparing to TFs in normal cells. Such genes fall into a few stress and response pathways. As a cancer advances, the level of involvement by direct DNA methylation in transcription regulation increases for majority of the cancer types examined.

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TRRUST: a reference database of human transcriptional regulatory interactions

Cited by 345 publications

References 37 publications

Toward a Reference Gene Catalog of Human Primary Monocytes

Toward a Reference Gene Catalog of Human Primary Monocytes

Take ACTION to characterize the functional identity of single cells

Transcription regulation by DNA methylation under stressful conditions in human cancer

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