Inverse Transformation Algorithm Code
Ontology highlight
ABSTRACT:
SUBMITTER: Vincent Wagner
PROVIDER: 812 | FAIRDOMHub | 2022-04-14
REPOSITORIES: FAIRDOMHub
Similar Datasets
Project description:Nucleosome conformation dictates the histone code
| PRJNA632919 | ENA
Project description:Deciphering the SUMO code in plants
| PRJNA1148947 | ENA
Project description:Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized “codes” that are read by specialized domains (reader domains) in chromatin associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP - histone PTM] specificity, and in doing so to decipher the histone code. However, this has largely been done using a reductive approach of isolated reader domains and histone peptides, with the assumption that PTM readout is unaffected by any higher order considerations. Here we show that histone PTM specificity is in fact dependent on nucleosomal context, necessitating we re-define the ‘histone code’ concept and further interrogate it at the nucleosomal level.
2021-05-06 | GSE150617 | GEO
Project description:How developmental signals program gene expression in space and time is still poorly understood. Here, we addressed this question for the plant master regulator, auxin. Transcriptional responses to auxin rely on a large multigenic transcription factor family, the auxin response factors (ARFs). We deconvoluted the complexity of ARF-regulated transcription using auxin-inducible synthetic promoters built from cis-element pair configurations differentially bound by ARFs. We demonstrate using cellular systems that ARF transcriptional properties are not only intrinsic but also depend on the cis-element pair configurations they bind to, thus identifying a bi-layer ARF/cis-element transcriptional code. Auxin-inducible synthetic promoters were expressed differentially in planta showing at single-cell resolution how this bi-layer code patterns transcriptional responses to auxin. Combining cis-element pair configurations in synthetic promoters created distinct patterns, demonstrating the combinatorial power of the auxin bi-layer code in generating diverse gene expression patterns that are not simply a direct translation of auxin distribution.
2025-07-31 | GSE241573 | GEO
Project description:Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and Decapentaplegic (DPP) pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation. Keywords: EGFR, BMP, gain/loss-of-function
2008-11-11 | GSE12477 | GEO
Project description:Next-generation sequencing (NGS) has supported precision therapeutic approaches that have improved the lives of children with rare diseases. Patients with congenital diarrhea and enteropathies (CODE) have a particularly difficult disease with high morbidity and mortality. However, there are now several targeted therapies including specific diets, pharmacological treatments, and surgical interventions that are based on an individual’s genetic diagnosis. We performed NGS on a large cohort of 139 infants with suspected monogenic congenital diarrheal disorders and identified known causal variants in 50% of cases, including a new founder NEUROG3 variant. We also uncovered and functionally characterized three novel CODE genes, GRWD1, MYO1A, and MON1A, using cell and zebrafish models.
2025-05-21 | GSE264461 | GEO
Project description:Epigenetic modifications and transcription factors form a chromatin code to regulate gene expression in many physiological and pathological processes. However, little is known about whether the environmental stimuli could interplay with this code and regulate the transcription and biological functions. Here, we interrogated the chromatin state of multiple epigenetic modifications and transcription factors during a time course of VEGF stimulation in the endothelial cells and found a broad change of transcriptome induced by VEGF. At the promoter-proximal regions, a unique epigenetic pattern of bivalent domain preferentially governed the part of transcriptome change by hijacking the EZH1 transcriptional activity. VEGF substantially altered the epigenetic landscape at enhancer regions and transcription factor chromatin occupancy across the genome, which significantly accounted for the change of VEGF-downstream gene expression. Moreover, by integrating a transcription-regulatory network of VEGF pathway, we discovered MAFs as a novel mater transcriptional factor controlling the VEGF transcriptional program and angiogenesis. Collectively, these results revealed the extracellular stimulus of VEGF in fact implements a significant reconfiguration of chromatin code that coordinately regulates the angiogenic response.
2018-03-28 | GSE109623 | GEO
Project description:Epigenetic modifications and transcription factors form a chromatin code to regulate gene expression in many physiological and pathological processes. However, little is known about whether the environmental stimuli could interplay with this code and regulate the transcription and biological functions. Here, we interrogated the chromatin state of multiple epigenetic modifications and transcription factors during a time course of VEGF stimulation in the endothelial cells and found a broad change of transcriptome induced by VEGF. At the promoter-proximal regions, a unique epigenetic pattern of bivalent domain preferentially governed the part of transcriptome change by hijacking the EZH1 transcriptional activity. VEGF substantially altered the epigenetic landscape at enhancer regions and transcription factor chromatin occupancy across the genome, which significantly accounted for the change of VEGF-downstream gene expression. Moreover, by integrating a transcription-regulatory network of VEGF pathway, we discovered MAFs as a novel mater transcriptional factor controlling the VEGF transcriptional program and angiogenesis. Collectively, these results revealed the extracellular stimulus of VEGF in fact implements a significant reconfiguration of chromatin code that coordinately regulates the angiogenic response.
2018-03-28 | GSE109625 | GEO
Project description:Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and Decapentaplegic (DPP) pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation. Keywords: EGFR, BMP, gain/loss-of-function RNA was isolated from hand dissected, stage 9-10 egg chambers. Five genetic backgrounds were profiled including: wild type, EGFR gain of function, EGFR loss of function, BMP gain of function, and BMP loss of function. Three biological replicates were hybridized for each pathway perturbation. The samples were split across two rounds of hybridization. Each round of hybridizations included three biological replicates for wild type: The first round included EGFR gof, EGFR lof, BMP gof, and wild type controls A1-A3 (GSM313514-16). For these 12 arrays the extraction, labeling, and hybridization steps were done in parallel. The second round included the BMP lof and wild type controls B1-B3 (GSM313517-19). For these 6 arrays, the extraction, labeling, and hybridization steps were done in parallel.
2008-11-11 | E-GEOD-12477 | biostudies-arrayexpress
Project description:Histone code dynamics during nitrogen response in tomato
| PRJNA807664 | ENA