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PubMed2000

Characterization of novel proteins based on known protein structures.

The genome sciences face the challenge to characterize structure and function of a vast number of novel genes. Sequence search techniques are used to infer functional and structural information from similarities to experimentally characterized genes or proteins. The persistent goal is to refine these techniques and to develop alternative and complementary methods to increase the range of reliable inference.Here, we focus on the structural and functional assignments that can be inferred from the known three-dimensional structures of proteins. The study uses all structures in the Protein Data Bank that were known by the end of 1997. The protein structures released in 1998 were then characterized in terms of functional and structural similarity to the previously known structures, yielding an estimate of the maximum amount of information on novel protein sequences that can be obtained from inference techniques. The 147 globular proteins corresponding to 196 domains released in 1998 have no clear sequence similarity to previously known structures. However, 75 % of the domains have extensive structure similarity to previously known folds, and most importantly, in two out of three cases similarity in structure coincides with related function. In view of this analysis, full utilization of existing structure data bases would provide information for many new targets even if the relationship is not accessible from sequence information alone. Currently, the most sophisticated techniques detect of the order of one-third of these relationships.

Amino Acid Sequence↗

PubMed2004

Modular epistasis in yeast metabolism.

Epistatic interactions, manifested in the effects of mutations on the phenotypes caused by other mutations, may help uncover the functional organization of complex biological networks. Here, we studied system-level epistatic interactions by computing growth phenotypes of all single and double knockouts of 890 metabolic genes in Saccharomyces cerevisiae, using the framework of flux balance analysis. A new scale for epistasis identified a distinctive trimodal distribution of these epistatic effects, allowing gene pairs to be classified as buffering, aggravating or noninteracting. We found that the ensuing epistatic interaction network could be organized hierarchically into function-enriched modules that interact with each other 'monochromatically' (i.e., with purely aggravating or purely buffering epistatic links). This property extends the concept of epistasis from single genes to functional units and provides a new definition of biological modularity, which emphasizes interactions between, rather than within, functional modules. Our approach can be used to infer functional gene modules from purely phenotypic epistasis measurements.

Algorithms↗

PubMed2006

ProtoBee: hierarchical classification and annotation of the honey bee proteome.

The recently sequenced genome of the honey bee (Apis mellifera) has produced 10,157 predicted protein sequences, calling for a computational effort to extract biological insights from them. We have applied an unsupervised hierarchical protein-clustering method, which was previously used in the ProtoNet system, to nearly 200,000 proteins consisting of the predicted honey bee proteins, the SWISS-PROT protein database, and the complete set of proteins of the mouse (Mus musculus) and the fruit fly (Drosophila melanogaster). The hierarchy produced by this method has been entitled ProtoBee. In ProtoBee, the proteins are hierarchically organized into 18,936 separate tree hierarchies, each representing a protein functional family. By using the mouse and Drosophila complete proteomes as reference, we are able to highlight functional groups of putative gene-loss events, putative novel proteins of unique functionality, and bee-specific paralogs. We have studied some of the ProtoBee findings and suggest their biological relevance. Examples include novel opsin genes and intriguing nuclear matches of mitochondrial genes. The organization of bee sequences into functional clusters suggests a natural way of automatically inferring functional annotation. Following this notion, we were able to assign functional annotation to about 70% of the sequences. ProtoBee is available at http://www.protobee.cs.huji.ac.il.

Animals↗

PubMed2003

Functional divergence in protein (family) sequence evolution.

As widely used today to infer 'function', the homology search is based on the neutral theory that sites of greatest functional significance are under the strongest selective constraints as well as lowest evolutionary rates, and vice versa. Therefore, site-specific rate changes (or altered selective constraints) are related to functional divergence during protein (family) evolution. In this paper, we review our recent work about this issue. We show a great deal of functional information can be obtained from the evolutionary perspective, which can in turn be used to facilitate high throughput functional assays. The emergence of evolutionary functional genomics is also indicated. The related software DIVERGE can be obtained from http://xgu1.zool.iastate.edu.

Amino Acid Sequence↗

PubMed2003

Whole-proteome interaction mining.

MOTIVATION: A major post-genomic scientific and technological pursuit is to describe the functions performed by the proteins encoded by the genome. One strategy is to first identify the protein-protein interactions in a proteome, then determine pathways and overall structure relating these interactions, and finally to statistically infer functional roles of individual proteins. Although huge amounts of genomic data are at hand, current experimental protein interaction assays must overcome technical problems to scale-up for high-throughput analysis. In the meantime, bioinformatics approaches may help bridge the information gap required for inference of protein function. In this paper, a previously described data mining approach to prediction of protein-protein interactions (Bock and Gough, 2001, Bioinformatics, 17, 455-460) is extended to interaction mining on a proteome-wide scale. An algorithm (the phylogenetic bootstrap) is introduced, which suggests traversal of a phenogram, interleaving rounds of computation and experiment, to develop a knowledge base of protein interactions in genetically-similar organisms. RESULTS: The interaction mining approach was demonstrated by building a learning system based on 1,039 experimentally validated protein-protein interactions in the human gastric bacterium Helicobacter pylori. An estimate of the generalization performance of the classifier was derived from 10-fold cross-validation, which indicated expected upper bounds on precision of 80% and sensitivity of 69% when applied to related organisms. One such organism is the enteric pathogen Campylobacter jejuni, in which comprehensive machine learning prediction of all possible pairwise protein-protein interactions was performed. The resulting network of interactions shares an average protein connectivity characteristic in common with previous investigations reported in the literature, offering strong evidence supporting the biological feasibility of the hypothesized map. For inferences about complete proteomes in which the number of pairwise non-interactions is expected to be much larger than the number of actual interactions, we anticipate that the sensitivity will remain the same but precision may decrease. We present specific biological examples of two subnetworks of protein-protein interactions in C. jejuni resulting from the application of this approach, including elements of a two-component signal transduction systems for thermoregulation, and a ferritin uptake network.

Algorithms↗

PubMed1982

Normal exercise capacity in patients with severe left ventricular dysfunction: compensatory mechanisms.

About one-third of patients who have severe left ventricular dysfunction can achieve normal levels of exercise. To elucidate the mechanisms that permit this to occur, we studied six patients with severe left ventricular dysfunction (average left ventricular ejection fraction 17 +/- 2.5% [mean +/- SEM]) who achieved nearly normal levels of exercise tolerance (greater than 11 minutes of treadmill exercise, Sheffield protocol). All patients had normal pulmonary function at rest and during exercise. Hemodynamics were measured at rest and during supine and upright exercise. The major mechanisms of the preserved exercise capacity in these patients were chronotropic competence, ability to tolerate elevated wedge pressures (33 +/- 3 mm Hg) without dyspnea, ventricular dilation, and increased levels of plasma norepinephrine at rest and during exercise. Also, whereas peripheral vascular resistance was unchanged during supine exercise, it decreased by 50% during similar levels of upright exercise. As a consequence, increases in cardiac output from rest to exercise were greater during upright than supine exercise (100% vs 50%, respectively) (p less than 0.05), and pulmonary wedge pressures were lower during upright than supine exercise (21 +/- 5 mm Hg vs 33 +/- 3 mm Hg). Thus, multiple mechanisms permit some patients with severe left ventricular dysfunction to achieve normal levels of exercise. These studies emphasize that left ventricular function must be assessed by direct means rather than inferring function of the left ventricle from the results of an exercise tolerance test.

Aged↗

PubMed2001

Dynamic diaschisis: anatomically remote and context-sensitive human brain lesions.

Functional neuroimaging was used to investigate how lesions to the Broca's area impair neuronal responses in remote undamaged cortical regions. Four patients with speech output problems, but relatively preserved comprehension, were scanned while viewing words relative to consonant letter strings. In normal subjects, this results in left lateralized activation in the posterior inferior frontal, middle temporal, and posterior inferior temporal cortices. Each patient activated normally in the middle temporal region but abnormally in the damaged posterior inferior frontal cortex and the undamaged posterior inferior temporal cortex. In the damaged frontal region, activity was insensitive to the presence of words but in the undamaged posterior inferior temporal region, activity decreased in the presence of words rather than increasing as it did in the normal individuals. The reversal of responses in the left posterior inferior temporal region illustrate the context-sensitive nature of the abnormality and that failure to activate the left posterior temporal region could not simply be accounted for by insufficient demands on the underlying function. We propose that, in normal individuals, visual word presentation changes the effective connectivity among reading areas and, in patients, posterior temporal responses are abnormal when they depend upon inputs from the damaged inferior frontal cortex. Our results serve to introduce the concept of dynamic diaschisis; the anatomically remote and context-sensitive effects of focal brain lesions. Dynamic diaschisis reveals abnormalities of functional integration that may have profound implications for neuropsychological inference, functional anatomy and, vicariously, cognitive rehabilitation.

Aphasia, Broca↗

PubMed2026

FANTASIA suite: a reproducible and configurable framework for embedding-based functional annotation of proteins.

Embedding-based annotation transfer is increasingly used for protein function inference due to protein language models capture sequence, structural, and functional signals that may extend beyond conventional pairwise similarity. However, systematic application of these approaches requires control over model choice, reference composition, lookup parameters, evidence traceability, and output formats. We developed the FANTASIA suite, a configurable framework for embedding-based functional annotation of proteins. The suite combines a database-backed implementation for reproducible and extensible analyses with a portable flat-file implementation for rapid local annotation and pipeline integration. Using non-model and model-organism proteomes, we show that larger neighbourhood sizes remain practical for proteome-scale analyses and that taxonomy and sequence-identity filtering support leakage-aware benchmarking. We also compare the supported models with baseline methods through external CAFA5 evaluation and provide practical guidance based on empirical evidence variables. FANTASIA provides a controlled, scalable, and reproducible framework for extending functional annotation across the rapidly expanding diversity of sequenced organisms.

Software↗

PubMed2006

Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes.

MOTIVATION: We compare phylogenetic approaches for inferring functional gene links. The approaches detect independent instances of the correlated gain and loss of pairs of genes from species' genomes. We investigate the effect on results of basing evidence of correlations on two phylogenetic approaches, Dollo parsminony and maximum likelihood (ML). We further examine the effect of constraining the ML model by fixing the rate of gene gain at a low value, rather than estimating it from the data. RESULTS: We detect correlated evolution among a test set of pairs of yeast (Saccharomyces cerevisiae) genes, with a case study of 21 eukaryotic genomes and test data derived from known yeast protein complexes. If the rate at which genes are gained is constrained to be low, ML achieves by far the best results at detecting known functional links. The model then has fewer parameters but it is more realistic by preventing genes from being gained more than once. AVAILABILITY: BayesTraits by M. Pagel and A. Meade, and a script to configure and repeatedly launch it by D. Barker and M. Pagel, are available at http://www.evolution.reading.ac.uk

Algorithms↗

PubMed2026

scGPA: an LLM-assisted workflow for directional virtual gene perturbation analysis from single-cell transcriptomes.

BACKGROUND: Existing virtual perturbation methods can often infer directional changes by comparing predicted post-perturbation expression profiles with control cells. However, workflows that directly return direction-specific downstream candidate genes together with confidence scores, evidence support and interpretable summaries remain limited. We developed scGPA, an LLM-assisted workflow system for directional single-cell virtual gene perturbation analysis. METHODS: scGPA starts from raw single-cell RNA sequencing data and performs quality control, normalization, dimensionality reduction, clustering and cell-group selection. It then constructs cell-group-specific wild-type regulatory networks using repeated subsampling, principal component regression (PCR)/Ridge-based network inference and CP tensor denoising. Based on these networks, scGPA simulates dose-aware virtual knockdown of the target gene and applies signed perturbation propagation to estimate the magnitude and direction of downstream transcriptional responses. LLM assistance is used for marker-based cell-type annotation, evidence-guided candidate prioritization and user-facing biological summarization. RESULTS: We benchmarked scGPA across five public Perturb-seq datasets and compared its performance with GEARS, scGPT and a random baseline. The overall correct prediction rate of scGPA was 23.0%, exceeding those of GEARS (20.7%), scGPT (15.1%) and the random baseline (13.6%). These results indicate that scGPA achieved a higher correct prediction rate than the two comparator models and the random baseline. We subsequently evaluated scGPA using a public osteosarcoma single-cell dataset and performed qRT-PCR validation in 143B osteosarcoma cells. Among genes with significant experimental changes, scGPA achieved a directional concordance of 76.9%. When all tested downstream genes were counted, 37.0% were directionally correct, 51.9% showed no significant change and 11.1% changed in the opposite direction. CONCLUSIONS: scGPA provides a practical workflow system for predicting and prioritizing direction-specific downstream transcriptional responses after target-gene perturbation. By integrating single-cell regulatory network inference, signed virtual perturbation and LLM-assisted interpretation, scGPA supports target-gene function inference and downstream mechanistic investigation from single-cell transcriptomic data.

Single-Cell Gene Expression Analysis↗

PubMed1992

[Approach to studying natural oligopeptides in the area of structure relationship to function].

Structure and structure-function relations of naturally occurring oligopeptides and peptide receptors are discussed. An approach to inferring function of low-molecular peptides in the direction from their structure is postulated. Diverse biological activities of oligopeptides supposedly arise from a limited number of preferable spatial structures which may exist under physiological conditions. Each particular function of an oligopeptide is connected with a definite spatial structure, belonging to the set of the low-energy conformations. A method is suggested for constructing a synthetic analogue with a predetermined physiologically active conformation, prior to all chemical and biological tests.

Oligopeptides↗

PubMed2003

Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach.

The genome of Mycobacterium tuberculosis was analyzed using recently developed computational approaches to infer protein function and protein linkages. We evaluated and employed a method to infer genes likely to belong to the same operon, as judged by the nucleotide distance between genes in the same genomic orientation, and combined this method with those of the Rosetta Stone, Phylogenetic Profile and conserved Gene Neighbor computational methods for the inference of protein function.

Bacterial Proteins↗

PubMed2003

Efficient identification of side-chain patterns using a multidimensional index tree.

Convergent evolution often produces similar functional sites in nonhomologous proteins. The identification of these sites can make it possible to infer function from structure, to pinpoint the location of a functional site, to identify enzymes with similar enzymatic mechanisms, or to discover putative functional sites. In this article, a novel method is presented that (a) queries a database of protein structures for the occurrence of a given side chain pattern and (b) identifies interesting side-chain patterns in a given structure. For efficiency and to make a robust statistical evaluation of the significance of a similarity possible, patterns of three residues (or triads) are considered. Each triad is encoded as a high-dimensional vector and stored in an SR (Sphere/Rectangle) tree, an efficient multidimensional index tree. Identifying similar triads can then be reformulated as identifying neighboring vectors. The method deals with many features that otherwise complicate the identification of meaningful patterns: shifted backbone positions, conservative substitutions, various atom label ambiguities and mirror imaged geometries. The combined treatment of these features leads to the identification of previously unidentified patterns. In particular, the identification of mirror imaged side-chain patterns is unique to the here-described method. Interesting triads in a given structure can be identified by extracting all triads and comparing them with a database of triads involved in ligand binding. The approach was tested by an all-against-all comparison of unique representatives of all SCOP superfamilies. New findings include mirror imaged metal binding and active sites, and a putative active site in bacterial luciferase.

3-Isopropylmalate Dehydrogenase↗

PubMed2006

A critique of functional localisers.

In this critique, we review the usefulness of functional localising scans in functional MRI studies. We consider their conceptual motivations and the implications for experimental design and inference. Functional localisers can often be viewed as acquiring data from cells that have been removed from an implicit factorial design. This perspective reveals their potentially restrictive nature. We deconstruct two examples from the recent literature to highlight the key issues. We conclude that localiser scans can be unnecessary and, in some instances, lead to a biased and inappropriately constrained characterisation of functional anatomy.

Brain Mapping↗

PubMed1998

Reveal, a general reverse engineering algorithm for inference of genetic network architectures.

Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.

Algorithms↗

PubMed2005

Reciprocal evolution of the cerebellum and neocortex in fossil humans.

Human brain evolution involved both neurological reorganization and an increase in overall brain volume relative to body mass. It is generally difficult to draw functional inferences about the timing and nature of brain reorganization, given that superficial brain morphology recorded on fossil endocasts is functionally ambiguous. However, the cerebellum, housed in the clearly delineated posterior cranial fossa, is functionally and ontologically discrete. The cerebellum is reciprocally connected to each of 14 neocortical regions important to human cognitive evolution. Cerebellar volume varies significantly relative to overall brain volume among mammalian orders, as well as within the primate order. There is also significant diachronic variation among fossil human taxa. In the australopithecines and early members of the genus Homo, the cerebral hemispheres were large in proportion to the cerebellum, compared with other hominoids. This trend continued in Middle and Late Pleistocene humans, including Neandertals and Cro-Magnon 1, who have the largest cerebral hemispheres relative to cerebellum volume of any primates, including earlier and Holocene humans. In recent humans, however, the pattern is reversed; the cerebellum is larger with respect to the rest of the brain (and, conversely, the cerebral hemispheres are smaller with respect to the cerebellum) than in Late Pleistocene humans. The cerebellum and cerebral hemispheres appear to have evolved reciprocally. Cerebellar development in Holocene humans may have provided greater computational efficiency for coping with an increasingly complex cultural and conceptual environment.

Biological Evolution↗

PubMed1998

hyp loci control cell pattern formation in the vegetative mycelium of Aspergillus nidulans.

Aspergillus nidulans grows by apical extension of multinucleate cells called hyphae that are subdivided by the insertion of crosswalls called septa. Apical cells vary in length and number of nuclei, whereas subapical cells are typically 40 microm long with three to four nuclei. Apical cells have active mitotic cycles, whereas subapical cells are arrested for growth and mitosis until branch formation reinitiates tip growth and nuclear divisions. This multicellular growth pattern requires coordination between localized growth, nuclear division, and septation. We searched a temperature-sensitive mutant collection for strains with conditional defects in growth patterning and identified six mutants (designated hyp for hypercellular). The identified hyp mutations are nonlethal, recessive defects in five unlinked genes (hypA-hypE). Phenotypic analyses showed that these hyp mutants have aberrant patterns of septation and show defects in polarity establishment and tip growth, but they have normal nuclear division cycles and can complete the asexual growth cycle at restrictive temperature. Temperature shift analysis revealed that hypD and hypE play general roles in hyphal morphogenesis, since inactivation of these genes resulted in a general widening of apical and subapical cells. Interestingly, loss of hypA or hypB function lead to a cessation of apical cell growth but activated isotropic growth and mitosis in subapical cells. The inferred functions of hypA and hypB suggest a mechanism for coordinating apical growth, subapical cell arrest, and mitosis in A. nidulans.

Aspergillus nidulans↗

PubMed1998

Identification of divergent functions in homologous proteins by induction over conserved modules.

Homologous proteins do not necessarily exhibit identical biochemical function. Despite this fact, local or global sequence similarity is widely used as an indication of functional identity. Of the 1327 Enzyme Commission defined functional classes with more than one annotated example in the sequence databases, similarity scores alone are inadequate in 251 (19%) of the cases. We test the hypothesis that conserved domains, as defined in the ProDom database, can be used to discriminate between alternative functions for homologous proteins in these cases. Using machine learning methods, we were able to induce correct discriminators for more than half of these 251 challenging functional classes. These results show that the combination of modular representations of proteins with sequence similarity improves the ability to infer function from sequence over similarity scores alone.

Alcohol Dehydrogenase↗