Ke-Estimation used in the article

Ke-Estimation used in the articl

A brief summary for the stabilizing analysis of the fundamental subsystems without regulation.

<p>A brief summary for the stabilizing analysis of the fundamental subsystems without regulation.</p

The whole process of fusion used in the mathematical model is shown.

<p>One direction arrows and symbol of represent the reaction between proteins, ions and complexes, while full direction arrows connect two parts of a single reaction. Modified from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038699#pone.0038699-Weber1" target="_blank">[1]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038699#pone.0038699-Burgoyne2" target="_blank">[6]</a>.</p

Reaction rates for the fundamental subsystem.

<p>Note: is the reaction rate for ; is for ; is for , is for , and is the fusion-concentration constant.</p

A comparison to the good-of-fit level between the numerical results by the inverse problem analysis and the original experimental data from [9].

<p>The error is about .</p

The Evolutionary Panorama of Organ-Specifically Expressed or Repressed Orthologous Genes in Nine Vertebrate Species

<div><p>RNA sequencing (RNA-Seq) technology provides the detailed transcriptomic information for a biological sample. Using the RNA-Seq data of six organs from nine vertebrate species, we identified a number of organ-specifically expressed or repressed orthologous genes whose expression patterns are mostly conserved across nine species. Our analyses show the following results: (i) About 80% of these genes have a chordate or more ancient origin and more than half of them are the legacy of one or multiple rounds of large-scale gene duplication events. (ii) Their evolutionary rates are shaped by the organ in which they are expressed or repressed, e.g. the genes specially expressed in testis and liver generally evolve more than twice as fast as the ones specially expressed in brain and cerebellum. The organ-specific transcription factors were discriminated from these genes. The ChIP-seq data from the ENCODE project also revealed the transcription-related factors that might be involved in regulating human organ-specifically expressed or repressed genes. Some of them are shared by all six human organs. The comparison of ENCODE data with mouse/chicken ChIP-seq data proposes that organ-specifically expressed or repressed orthologous genes are regulated in various combinatorial fashions in different species, although their expression features are conserved among these species. We found that the duplication events in some gene families might help explain the quick organ/tissue divergence in vertebrate lineage. The phylogenetic analysis of testis-specifically expressed genes suggests that some of them are prone to develop new functions for other organs/tissues.</p></div

Phylogenetic tree of MACC1 gene family.

<p>A <i>Ciona intestinalis</i> gene was selected as the outgroup to root the tree and only the cladogram is shown. The tree node where a possible large-scale duplication event happened is marked with a filled black square ■. 7 means the gene’s expression level is higher than 95% of all genes expressed in the organ. 6 is between 95% and 85%. 5 is between 85% and 65%. 4 is between 65% and 35%. 3 is between 35% and 15%. 2 is between 15% and 5%. 1 is lower than 5%. 0 means no expression at all. N is not available.</p

Five most common transcription-related factors might be involved in regulating OSER genes.

<p>Five most common transcription-related factors might be involved in regulating OSER genes.</p

Distribution of the number orthologous clusters in the gene families containing OSER genes.

<p>Distribution of the number orthologous clusters in the gene families containing OSER genes.</p

Classification of OSER clusters according to their evolutionary origins.

<p>Classification of OSER clusters according to their evolutionary origins.</p