Navigation Links
UC San Diego researchers use metagene 'portraits' to reveal distinct stages of kidney formation

In the art world, the most successful portraits are often those that reveal the true essence of the subject a subject that on canvas, at least, will never age. In the science world, researchers are relying on portraits of gene expression patterns but, in this case, the images are helping to reveal how various tissues form.

Now, a multi-disciplinary team at UC San Diego has used novel computational methods to gain insight into kidney formation. By performing time-series analyses of global gene expression, and clustering these genes into larger groups known as metagene portraits and also calculating entropy values, the researchers have identified distinct stages of organ formation.

The research, published in the December 9 edition of Science Signaling, is also significant in that it suggests additional genes that had not been previously implicated in orchestration of kidney development.

"The approach may also be helpful for understanding tissue regeneration and pathological states," said Sanjay K. Nigam, Professor of UC San Diego's Department of Pediatrics, Department of Medicine (Nephrology-Hypertension) and the Department of Cellular and Molecular Medicine. "Analysis of the metagene portraits suggested points of stability and transition which are not as evident using conventional methods."

Additional research members in the study include Igor F. Tsigelny, a project scientist with UC San Diego's Department of Chemistry and Biochemistry and the San Diego Supercomputer Center at UC San Diego; and Valentina L. Kouznetsova; Derina E. Sweeney; Wei Wu; and Kevin T. Bush; all with UC San Diego's School of Medicine.

In efforts to provide a more comprehensive view of organogenesis, the researchers compared and analyzed visual representations of gene expression patterns during kidney development. Approximately 30,000 genes were organized into 650 groups called metagenes, or gene clusters known as self-organizing maps (SOMs).

Essentially acting as unsupervised learning neural networks, SOMs cluster genes with similar temporal expression profiles into metagene portraits. In this case, the SOMs were collected using microarray gene expression data and a high-dimensional data analysis program called Gene Expression Dynamics Inspector, or GEDI. UC San Diego scientists then performed a detailed time-series analysis of the kidney SOMs reflecting various stages of organogenesis. That was followed by entropy calculations for each SOM to measure the differences in states during the various stages, before correlating these results with morphometric parameters and specific gene networks.

Taken together, analysis of the metagene portraits suggested that kidney formation could be divided into as many as eight distinct stages.

"Although there is morphological support for the notion of stages, the beginning and end points of those stages can be difficult to define because many basic morphogenetic processes occur simultaneously," said Tsigelny. "Our research suggests that with the metagene analysis and entropy calculations, global gene expression can be used to more clearly define these stages and allow us to have a fuller understanding about how organs form."


Contact: Jan Zverina
University of California - San Diego

Related biology news :

1. Field-hospital-on-a-chip project awarded to nanoengineer from UC San Diego
2. San Diego Supercomputer Center and UCSD announce Triton Resource
3. UC San Diego bioengineers fill holes in science of cellular self-organization
4. NIH doles out $3M in new innovator awards to 2 UC San Diego faculty
5. Generation innovation: Young UC San Diego bioengineer to use NIH grant to fuel tissue engineering
6. UC San Diego researchers could help US military thwart explosive threats
7. UC San Diego launches Institute of Engineering in Medicine to accelerate health care tech
8. UC San Diego researchers identify potential new drug candidates to combat bird flu
9. Glowing films developed by UC San Diego chemists reveal traces of explosives
10. UC San Diego researchers eliminate drug discovery bottleneck
11. Biologists at UC San Diego identify key protein in cells self-eating function
Post Your Comments:
(Date:6/22/2016)... On Monday, the Department of Homeland Security (DHS) issued ... the Biometric Exit Program. The Request for Information (RFI), ... that CBP intends to add biometrics to confirm when ... , in order to deter visa overstays, to ... Logo - ...
(Date:6/20/2016)... 20, 2016 Securus Technologies, a leading ... for public safety, investigation, corrections and monitoring announced ... it has secured the final acceptance by all ... Managed Access Systems (MAS) installed. Furthermore, Securus will ... be installed by October, 2016. MAS distinguishes between ...
(Date:6/15/2016)... New York , June 15, 2016 /PRNewswire/ ... a new market report titled "Gesture Recognition Market by ... and Forecast, 2016 - 2024". According to the report, ... USD 11.60 billion in 2015 and is estimated ... reach USD 48.56 billion by 2024.  ...
Breaking Biology News(10 mins):
(Date:6/24/2016)... ... June 24, 2016 , ... While the majority of commercial spectrophotometers and ... and the 6000i models are higher end machines that use the more unconventional z-dimension ... light beam from the bottom of the cuvette holder. , FireflySci has developed ...
(Date:6/23/2016)... June 23, 2016   Boston Biomedical , ... compounds designed to target cancer stemness pathways, announced ... granted Orphan Drug Designation from the U.S. Food ... gastric cancer, including gastroesophageal junction (GEJ) cancer. Napabucasin ... to inhibit cancer stemness pathways by targeting STAT3, ...
(Date:6/23/2016)... ... June 23, 2016 , ... Charm Sciences, ... microbial test has received AOAC Research Institute approval 061601. , “This is another ... year,” stated Bob Salter, Vice President of Regulatory and Industrial Affairs. “The Peel ...
(Date:6/23/2016)... ... ... Supplyframe, the Industry Network for electronics hardware design and ... in Pasadena, Calif., the Design Lab’s mission is to bring together inventors and ... brought to market. , The Design Lab is Supplyframe’s physical representation of one ...
Breaking Biology Technology: