TFClass: an expandable hierarchical classification of human transcription factors

Wingender, Edgar; Schoeps, Torsten; Dönitz, Jürgen

doi:10.1093/nar/gks1123

Cited by 149 publications

(176 citation statements)

References 30 publications

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“…We scanned peaks for individual motif occurrences with FIMO 42 (parameters --thresh .00001, --max-stored-scores 500000, and a first-order background model). In addition to leveraging motifs of human TF orthologs, we increased the mouse TF coverage of our motif database by additionally considering TF family subclasses 43 . We took advantage of similarities among TF subfamily sequence preferences to detect potential binding events of poorly characterized TF subfamily members.…”

Section: Methodsmentioning

confidence: 99%

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation

et al. 2017

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Type 1 regulatory T (Tr1) cells are induced by interleukin-27 (IL-27) and have critical roles in the control of autoimmunity and resolution of inflammation. Here, we show that the transcription factors IRF1 and BATF are induced early during treatment with IL-27 and are required for the differentiation and function of Tr1 cells in vitro and in vivo. Epigenetic and transcriptional analyses reveal that both transcription factors influence chromatin accessibility and expression of genes required for Tr1 cell function. IRF1 and BATF deficiencies uniquely alter the chromatin landscape, suggesting that these factors serve a pioneering function during Tr1 cell differentiation.

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Section: Methodsmentioning

confidence: 99%

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation

et al. 2017

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“…Among 1,762 human and 1,516 mouse transcription factors compiled from the literature 21–23 , promoter level expression profiles for 1,665 human transcription factors (94%) and 1,382 mouse transcription factors (91%) were obtained (Supplementary Tables 7, 8 and 9 and Supplementary Note 6). The distribution of expression levels and cell-type or tissue-specificity of transcription factors (Extended Data Fig.…”

Section: Key Cell-type-specific Transcription Factorsmentioning

confidence: 99%

A promoter-level mammalian expression atlas

Forrest¹,

Kawaji²,

Rehli³

et al. 2014

Nature

1,835

1,597

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Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

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“…We compared 699 pairs of human-mouse orthologous TFs that were separately obtained from TFClass (Wingender et al, 2013) and TFdb (Kanamori et al, 2004) databases. Most (82.83%) of these human-mouse orthologous TF pairs were highly conserved in terms of gene sequence identity 80%.…”

Section: Expression Similarities and Differences Of Orthologous Transmentioning

confidence: 99%

“…For comparing orthologous human-mouse genes, we also obtained the GC content, alternative splicing modes and identities of human-mouse orthologous pairs using Ensembl BioMart. To investigate the orthologous human-mouse TF (transcription factor) genes, we also downloaded the human and mouse TFs from TFClass (Wingender et al, 2013) and TFdb (Kanamori et al, 2004) databases, respectively. Those TFs of human and mouse that are not orthologous pairs were excluded.…”

Section: Public Data Used In the Studymentioning

confidence: 99%

Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos

Chen

Yang

et al. 2016

Sci. China Life Sci.

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Human and mouse orthologs are expected to have similar biological functions; however, many discrepancies have also been reported. We systematically compared human and mouse orthologs in terms of alternative splicing patterns and expression profiles. Human-mouse orthologs are divergent in alternative splicing, as human orthologs could generally encode more isoforms than their mouse orthologs. In early embryos, exon skipping is far more common with human orthologs, whereas constitutive exons are more prevalent with mouse orthologs. This may correlate with divergence in expression of splicing regulators. Orthologous expression similarities are different in distinct embryonic stages, with the highest in morula. Expression differences for orthologous transcription factor genes could play an important role in orthologous expression discordance. We further detected largely orthologous divergence in differential expression between distinct embryonic stages. Collectively, our study uncovers significant orthologous divergence from multiple aspects, which may result in functional differences and dynamics between human-mouse orthologs during embryonic development. ortholog, alternative splicing, RNA-seq, early embryo, gene expression Citation:

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TFClass: an expandable hierarchical classification of human transcription factors

Cited by 149 publications

References 30 publications

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation

A promoter-level mammalian expression atlas

Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos

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