8 research outputs found
The recognition results of discontinuous domains at various TS-score and SI cutoffs.
<p>(A) MCC; (B) Recall; (C) Precision (5 parallel lines show the boundaries of the precision region at different b values). (D) The figure of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141541#pone.0141541.e009" target="_blank">Eq 6</a>.</p
An illustration of the procedure to generate the samples.
<p>A 3-domain chain is defined as (A1A2)(B)(C). A1 and A2 form one structure domain, while B and C are independent domain, respectively. The (A1A1) is treated as “Positive” sample; (A1C) and (BC) as “Negative” and other combinations are ignored.</p
The benchmark results of DomEx with domain boundary predictors.
<p>The methods with discontinuous domain detection are shown as dark bars.</p
The comparison of the templates from CATH+SCOP, Pfam and CATH+SCOP+PFAM.
<p>(A) Precision comparison; (B) The proportion of templates coming from CATH+SCOP and Pfam as parameter b varies.</p
The training and validation results using <i>T</i><sub><i>SI</i></sub> = <i>f</i>(<i>T</i><sub><i>TS</i></sub>,<i>b</i>) constraints.
<p>The cutoff <i>T</i><sub><i>TS</i></sub> (for TS-score) and <i>T</i><sub><i>SI</i></sub> (for SI) in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141541#pone.0141541.g005" target="_blank">Fig 5</a> are constrained by <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141541#pone.0141541.e009" target="_blank">Eq 6</a>. (A) The results on the Training Dataset with parameter b from 0.9 to 0.1; (B) The results on the Validation Dataset with parameter b from 0.9 to 0.1, respectively.</p
The cases of N- to C-termini assembly.
<p>(A) The 3D structure of PDB: 1axkB. The two segments of the discontinuous domain (1–156|342–393) are colored in magenta and lemon green, respectively. (B) The 3D structure of PDB:1u0aD. It is an AB type Segment-Swapping Domain. (C) The 3D structure of PDB:1cpmA. It is a BA type Segment-Swapping Domain.</p
Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project
Alternative splicing allows a single
gene to produce multiple transcript-level
splice isoforms from which the translated proteins may show differences
in their expression and function. Identifying the major functional
or canonical isoform is important for understanding gene and protein
functions. Identification and characterization of splice isoforms
is a stated goal of the HUPO Human Proteome Project and of neXtProt.
Multiple efforts have catalogued splice isoforms as “dominant”,
“principal”, or “major” isoforms based
on expression or evolutionary traits. In contrast, we recently proposed
highest connected isoforms (HCIs) as a new class of canonical isoforms
that have the strongest interactions in a functional network and revealed
their significantly higher (differential) transcript-level expression
compared to nonhighest connected isoforms (NCIs) regardless of tissues/cell
lines in the mouse. HCIs and their expression behavior in the human
remain unexplored. Here we identified HCIs for 6157 multi-isoform
genes using a human isoform network that we constructed by integrating
a large compendium of heterogeneous genomic data. We present examples
for pairs of transcript isoforms of <i>ABCC3, RBM34</i>, <i>ERBB2</i>, and <i>ANXA7</i>. We found that functional
networks of isoforms of the same gene can show large differences.
Interestingly, differential expression between HCIs and NCIs was also
observed in the human on an independent set of 940 RNA-seq samples
across multiple tissues, including heart, kidney, and liver. Using
proteomic data from normal human retina and placenta, we showed that
HCIs are a promising indicator of expressed protein isoforms exemplified
by <i>NUDFB6</i> and <i>M6PR</i>. Furthermore,
we found that a significant percentage (20%, <i>p</i> =
0.0003) of human and mouse HCIs are homologues, suggesting their conservation
between species. Our identified HCIs expand the repertoire of canonical
isoforms and are expected to facilitate studying main protein products,
understanding gene regulation, and possibly evolution. The network
is available through our web server as a rich resource for investigating
isoform functional relationships (http://guanlab.ccmb.med.umich.edu/hisonet). All MS/MS data were available at ProteomeXchange Web site (http://www.proteomexchange.org) through their identifiers (retina:
PXD001242, placenta: PXD000754)