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Related Concept Videos

Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA (lncRNA)...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

Updated: Jun 3, 2026

Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets
03:37

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Published on: March 1, 2024

LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide

Geert Geeven1, Harold D Macgillavry, Ruben Eggers

  • 1Department of Mathematics, Faculty of Sciences, VU University, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.

Nucleic Acids Research
|March 23, 2011
PubMed
Summary

A new method, log-linear modeling of 3D contingency tables (LLM3D), accurately predicts transcription factor binding sites. LLM3D improves gene regulatory network reconstruction in mammals, identifying key regulators in yeast, stem cells, and neuron regeneration.

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Last Updated: Jun 3, 2026

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Genomics

Background:

  • Cellular processes rely on transcription factor (TF) interactions with target genes.
  • Reconstructing mammalian gene regulatory networks (GRNs) requires accurate TF binding site prediction.
  • Existing methods often struggle with the complexity of mammalian systems.

Purpose of the Study:

  • To introduce a novel computational method, log-linear modeling of 3D contingency tables (LLM3D), for predicting functional TF binding sites.
  • To demonstrate LLM3D's superiority over existing enrichment-based methods in identifying regulatory interactions.
  • To validate LLM3D's applicability in diverse biological contexts, including yeast, stem cells, and mammalian neurons.

Main Methods:

  • LLM3D integrates gene expression data, gene ontology (GO) annotations, and predicted TF binding sites.
  • A single statistical analysis framework is employed.
  • The method is tested on yeast metabolic cycle, mouse embryonic stem cell (mESC) self-renewal, and a mammalian neuron injury model.

Main Results:

  • LLM3D successfully identified novel transcriptional regulators of the yeast metabolic cycle.
  • It predicted key regulators of mESC self-renewal more accurately than existing methods.
  • LLM3D identified peroxisome proliferator-activated receptor γ (PPARγ) as a regulator of regenerative axon growth in injured mammalian neurons.

Conclusions:

  • LLM3D offers a significant methodological advancement for predicting functional TF regulatory interactions.
  • The method is effective even without experimental TF binding data.
  • LLM3D enhances the reconstruction of gene regulatory networks across different species and biological conditions.