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Integrative Analysis of Transcriptomics and Metabolomics

Creative Proteomics provides integrated analysis services of transcriptomics and metabolomics, exploring biological problems from two levels, verifying each other, screening key genes / metabolites / metabolic pathways from massive data, analyzing the development of biological systems process, explaining the complexity and wholeness of biological processes.

Why Do Integrative Analysis of Transcriptomics and Metabolomics?

Transcriptome sequencing can obtain a large number of differentially expressed genes and regulatory metabolic pathways. However, due to the difficulty in correlating genes and phenotypes, it is difficult to identify key signaling pathways, which often fails to achieve the expected research purposes. However, in contrast to other omics, metabolites reflect the true physiological state of an organism, and their changes lead directly to phenotypic changes. And the metabolome is most affected by the environment, and the impact of the environment on the organism is ultimately reflected in the changes of metabolites. For specific phenotypes such as physiology, pathology, growth and development, by combining the research methods of transcriptome and metabolome, we can integrate and analyze the information of many genes expressed in time series and differentially accumulated metabolite information; and combined with molecular biology techniques, we can explain the biological phenotype of interest from the molecular level, and explore the growth and development, physiological and pathological response mechanisms of organisms.

Our Integrative Analysis Services of Transcriptomics and Metabolomics

Creative Proteomics provides you with one-stop transcriptome sequencing services and metabolome testing services. In addition, we offer integrative analysis services of transcriptomics and metabolomics to seamlessly connect your experiments upstream and downstream.

Differential profiles of samples at gene expression level and metabolite level were obtained from transcriptome and metabolome data. However, transcription and metabolism in biological systems do not occur independently. In order to reveal the regulatory influence mechanism between gene expression and metabolites, we conducted integrative / association analysis of transcriptomics and metabolomics based on "genes or metabolites involved in the same biological process have the same or similar change rules".

Bioinformatics Analysis

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  • Excellent bioinformatics analysis: Our bioinformatics center brings together many high-level information analysis talents from home and abroad, and has many years of practical experience in the field of bioinformatics research and development.
  • Rich data analysis content: Standard analysis, advanced analysis, customized analysis.
  • In addition to excellent bioinformatics analysis, we also have an advanced experimental platform that supports sequencing and proteome / metabolome detection, etc., and we have many successful project experiences.
  • Cost-effective, short project cycle.


The results suggest that gibberellins and associated pathways are possibly developing the observed semi-dwarf pseudostem phenotype together with cell elongation and cell wall modification. The findings increase the understanding of the mechanisms underlying banana stem height and provide new clues for further dissection of specific gene functions.

Proposed model of the hormonal cross talk leading to the increase in pseudostem height in MT Aifen No. 1 banana.Fig.1 Proposed model of the hormonal cross talk leading to the increase in pseudostem height in MT Aifen No. 1 banana. Red arrow indicates the up (↑) or down (↓) regulated genes and red stars indicate that a putative interaction exists. (Deng G, et al., 2021)

Creative Proteomics relies on advanced platforms and cutting-edge technologies to provide omics services to customers around the world, and provide accurate and detailed analysis reports. In addition, we also provide multi-omics integrated analysis services. You can discuss with our technical engineers to customize solutions or build new methods to meet your specific needs. If you have any questions, you can tell us through the inquiry form, and our technicians will communicate with you. Please don't hesitate to contact us, Creative Proteomics can be trusted.


  1. Deng G, Bi F, Liu J, He W, Li C, Dong T, Yang Q, Gao H, Dou T, Zhong X, Peng M, Yi G, Hu C, Sheng O. Transcriptome and metabolome profiling provide insights into molecular mechanism of pseudostem elongation in banana. BMC Plant Biol. 2021 Mar 1;21(1):125. doi: 10.1186/s12870-021-02899-6. PMID: 33648452; PMCID: PMC7923470.

Case Study

Transcriptome and metabolome profiling provide insights into molecular mechanism of pseudostem elongation in banana

Journal: BMC Plant Biol
Impact factor: 4.215
Published: 2021 Mar


Banana plant height is an important trait for horticultural practices and semi-dwarf cultivars show better resistance to damages by wind and rain. However, the molecular mechanisms controlling the pseudostem height remain poorly understood. Herein, we studied the molecular changes in the pseudostem of a semi-dwarf banana mutant Aifen No. 1 (Musa spp. Pisang Awak sub-group ABB) as compared to its wild-type dwarf cultivar using a combined transcriptome and metabolome approach.

Materials & Methods

Semi-dwarf banana mutant Aifen No. 1 (Musa spp. Pisang Awak sub-group ABB) vs Wild-type dwarf cultivar

Transcriptome sequencing Metabolome testing Integrative analysis of transcriptome + metabolomics

127 differentially expressed genes

The differential regulation of genes related to the gibberellin pathway, auxin transport, cell elongation, and cell wall modification.

48 differentially accumulated metabolites

Metabolites belonging to amino acid and its derivatives, flavonoids, lignans, coumarins, organic acids, and phenolic acids were up-regulated in the mutant.

Based on the regulation of gibberellin and associated pathway-related genes, we discussed the involvement of gibberellins in pseudostem elongation in the mutant banana. Genes and metabolites associated with cell wall were explored and their involvement in cell extension is discussed.

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