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Related Concept Videos

Transcription01:17

Transcription

Transcription is the synthesis of RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in correctly synthesizing messenger RNA (mRNA). Transcriptional regulation is responsible for the differentiation of different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds of RNA Molecules
In eukaryotes,...
Transcription01:10

Transcription

Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
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...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
Master Transcription Regulators02:23

Master Transcription Regulators

Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...

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Related Experiment Video

Updated: Jul 10, 2026

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

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

Published on: March 1, 2024

Transcriptional target prediction using qualitative reasoning.

Li-San Wang1, Doris Wagner, Chang Seob Kwon

  • 1Dept. of Biol., Univ. of Pennsylvania, Philadelphia, PA 19104, USA.

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference
|October 20, 2007
PubMed
Summary

This study introduces a novel method to transform qualitative biological hypotheses into testable binary statements. This approach aids in predicting transcription targets from functional genomics data, performing comparably to existing methods.

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Area of Science:

  • Computational Biology
  • Genomics
  • Bioinformatics

Background:

  • Transcription target prediction commonly uses complex prior biological knowledge.
  • Existing methods struggle with qualitative biological hypotheses, which are difficult to quantify.
  • Many qualitative hypotheses can be broken down into binary logic statements.

Purpose of the Study:

  • To develop a new method for converting qualitative biological statements into quantitative, testable hypotheses.
  • To enable the prediction of transcription targets using functional genomics data and prior biological knowledge.
  • To provide a flexible and principled approach for testing biological hypotheses.

Main Methods:

  • Decomposition of qualitative biological hypotheses into a series of binary logic statements.
  • Generation of a partial ordering of outcomes from these binary statements.
  • Testing of the generated partial ordering using semi-parametric isotonic regression.

Main Results:

  • The developed method successfully converted qualitative statements into a testable framework.
  • Application to an Arabidopsis microarray dataset identified organ-specific transcriptional target genes.
  • Performance was comparable to existing methods, with added flexibility for complex criteria.

Conclusions:

  • The new method offers a robust way to integrate qualitative biological knowledge into transcription target prediction.
  • Semi-parametric isotonic regression provides a flexible yet principled statistical approach for hypothesis testing.
  • The algorithm facilitates rapid analysis of complex gene selection criteria in functional genomics studies.