Functional organization of the S. cerevisiae phosphorylation network.

Reversible protein phosphorylation is a signaling mechanism involved in all cellular processes. To create a systems view of the signaling apparatus in budding yeast, we generated an epistatic miniarray profile (E-MAP) comprised of 100,000 pairwise, quantitative genetic interactions, including virtually all protein and small-molecule kinases and phosphatases as well as key cellular regulators. Quantitative genetic interaction mapping reveals factors working in compensatory pathways (negative genetic interactions) or those operating in linear pathways (positive genetic interactions). We found an enrichment of positive genetic interactions between kinases, phosphatases, and their substrates. In addition, we assembled a higher-order map from sets of three genes that display strong interactions with one another: triplets enriched for functional connectivity. The resulting network view provides insights into signaling pathway regulation and reveals a link between the cell-cycle kinase, Cak1, the Fus3 MAP kinase, and a pathway that regulates chromatin integrity during transcription by RNA polymerase II.

On Expression Patterns and Developmental Origin of Human Brain Regions.

Anatomical substructures of the human brain have characteristic cell-types, connectivity and local circuitry, which are reflected in area-specific transcriptome signatures, but the principles governing area-specific transcription and their relation to brain development are still being studied. In adult rodents, areal transcriptome patterns agree with the embryonic origin of brain regions, but the processes and genes that preserve an embryonic signature in regional expression profiles were not quantified. Furthermore, it is not clear how embryonic-origin signatures of adult-brain expression interplay with changes in expression patterns during development. Here we first quantify which genes have regional expression-patterns related to the developmental origin of brain regions, using genome-wide mRNA expression from post-mortem adult human brains. We find that almost all human genes (92%) exhibit an expression pattern that agrees with developmental brain-region ontology, but that this agreement changes at multiple phases during development. Agreement is particularly strong in neuron-specific genes, but also in genes that are not spatially correlated with neuron-specific or glia-specific markers. Surprisingly, agreement is also stronger in early-evolved genes. We further find that pairs of similar genes having high agreement to developmental region ontology tend to be more strongly correlated or anti-correlated, and that the strength of spatial correlation changes more strongly in gene pairs with stronger embryonic signatures. These results suggest that transcription regulation of most genes in the adult human brain is spatially tuned in a way that changes through life, but in agreement with development-determined brain regions.

Gene Expression Switching of Receptor Subunits in Human Brain Development.

Synaptic receptors in the human brain consist of multiple protein subunits, many of which have multiple variants, coded by different genes, and are differentially expressed across brain regions and developmental stages. The brain can tune the electrophysiological properties of synapses to regulate plasticity and information processing by switching from one protein variant to another. Such condition-dependent variant switch during development has been demonstrated in several neurotransmitter systems including NMDA and GABA. Here we systematically detect pairs of receptor-subunit variants that switch during the lifetime of the human brain by analyzing postmortem expression data collected in a population of donors at various ages and brain regions measured using microarray and RNA-seq. To further detect variant pairs that co-vary across subjects, we present a method to quantify age-corrected expression correlation in face of strong temporal trends. This is achieved by computing the correlations in the residual expression beyond a cubic-spline model of the population temporal trend, and can be seen as a nonlinear version of partial correlations. Using these methods, we detect multiple new pairs of context dependent variants. For instance, we find a switch from GLRA2 to GLRA3 that differs from the known switch in the rat. We also detect an early switch from HTR1A to HTR5A whose trends are negatively correlated and find that their age-corrected expression is strongly positively correlated. Finally, we observe that GRIN2B switch to GRIN2A occurs mostly during embryonic development, presumably earlier than observed in rodents. These results provide a systematic map of developmental switching in the neurotransmitter systems of the human brain.

A unifying principle underlying the extracellular field potential spectral responses in the human cortex.

Electrophysiological mass potentials show complex spectral changes upon neuronal activation. However, it is unknown to what extent these complex band-limited changes are interrelated or, alternatively, reflect separate neuronal processes. To address this question, intracranial electrocorticograms (ECoG) responses were recorded in patients engaged in visuomotor tasks. We found that in the 10- to 100-Hz frequency range there was a significant reduction in the exponent χ of the 1/f(χ) component of the spectrum associated with neuronal activation. In a minority of electrodes showing particularly high activations the exponent reduction was associated with specific band-limited power modulations: emergence of a high gamma (80-100 Hz) and a decrease in the alpha (9-12 Hz) peaks. Importantly, the peaks' height was correlated with the 1/f(χ) exponent on activation. Control simulation ruled out the possibility that the change in 1/f(χ) exponent was a consequence of the analysis procedure. These results reveal a new global, cross-frequency (10-100 Hz) neuronal process reflected in a significant reduction of the power spectrum slope of the ECoG signal.

Auditory abstraction from spectro-temporal features to coding auditory entities.

The auditory system extracts behaviorally relevant information from acoustic stimuli. The average activity in auditory cortex is known to be sensitive to spectro-temporal patterns in sounds. However, it is not known whether the auditory cortex also processes more abstract features of sounds, which may be more behaviorally relevant than spectro-temporal patterns. Using recordings from three stations of the auditory pathway, the inferior colliculus (IC), the ventral division of the medial geniculate body (MGB) of the thalamus, and the primary auditory cortex (A1) of the cat in response to natural sounds, we compared the amount of information that spikes contained about two aspects of the stimuli: spectro-temporal patterns, and abstract entities present in the same stimuli such as a bird chirp, its echoes, and the ambient noise. IC spikes conveyed on average approximately the same amount of information about spectro-temporal patterns as they conveyed about abstract auditory entities, but A1 and the MGB neurons conveyed on average three times more information about abstract auditory entities than about spectro-temporal patterns. Thus, the majority of neurons in auditory thalamus and cortex coded well the presence of abstract entities in the sounds without containing much information about their spectro-temporal structure, suggesting that they are sensitive to abstract features in these sounds.

FuncISH: learning a functional representation of neural ISH images.

MOTIVATION: High-spatial resolution imaging datasets of mammalian brains have recently become available in unprecedented amounts. Images now reveal highly complex patterns of gene expression varying on multiple scales. The challenge in analyzing these images is both in extracting the patterns that are most relevant functionally and in providing a meaningful representation that allows neuroscientists to interpret the extracted patterns. RESULTS: Here, we present FuncISH--a method to learn functional representations of neural in situ hybridization (ISH) images. We represent images using a histogram of local descriptors in several scales, and we use this representation to learn detectors of functional (GO) categories for every image. As a result, each image is represented as a point in a low-dimensional space whose axes correspond to meaningful functional annotations. The resulting representations define similarities between ISH images that can be easily explained by functional categories. We applied our method to the genomic set of mouse neural ISH images available at the Allen Brain Atlas, finding that most neural biological processes can be inferred from spatial expression patterns with high accuracy. Using functional representations, we predict several gene interaction properties, such as protein-protein interactions and cell-type specificity, more accurately than competing methods based on global correlations. We used FuncISH to identify similar expression patterns of GABAergic neuronal markers that were not previously identified and to infer new gene function based on image-image similarities. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Specialization of gene expression during mouse brain development.

The transcriptome of the brain changes during development, reflecting processes that determine functional specialization of brain regions. We analyzed gene expression, measured using in situ hybridization across the full developing mouse brain, to quantify functional specialization of brain regions. Surprisingly, we found that during the time that the brain becomes anatomically regionalized in early development, transcription specialization actually decreases reaching a low, "neurotypic", point around birth. This decrease of specialization is brain-wide, and mainly due to biological processes involved in constructing brain circuitry. Regional specialization rises again during post-natal development. This effect is largely due to specialization of plasticity and neural activity processes. Post-natal specialization is particularly significant in the cerebellum, whose expression signature becomes increasingly different from other brain regions. When comparing mouse and human expression patterns, the cerebellar post-natal specialization is also observed in human, but the regionalization of expression in the human Thalamus and Cortex follows a strikingly different profile than in mouse.

Positive correlation between ADAR expression and its targets suggests a complex regulation mediated by RNA editing in the human brain.

A-to-I RNA editing by adenosine deaminases acting on RNA is a post-transcriptional modification that is crucial for normal life and development in vertebrates. RNA editing has been shown to be very abundant in the human transcriptome, specifically at the primate-specific Alu elements. The functional role of this wide-spread effect is still not clear; it is believed that editing of transcripts is a mechanism for their down-regulation via processes such as nuclear retention or RNA degradation. Here we combine 2 neural gene expression datasets with genome-level editing information to examine the relation between the expression of ADAR genes with the expression of their target genes. Specifically, we computed the spatial correlation across structures of post-mortem human brains between ADAR and a large set of targets that were found to be edited in their Alu repeats. Surprisingly, we found that a large fraction of the edited genes are positively correlated with ADAR, opposing the assumption that editing would reduce expression. When considering the correlations between ADAR and its targets over development, 2 gene subsets emerge, positively correlated and negatively correlated with ADAR expression. Specifically, in embryonic time points, ADAR is positively correlated with many genes related to RNA processing and regulation of gene expression. These findings imply that the suggested mechanism of regulation of expression by editing is probably not a global one; ADAR expression does not have a genome wide effect reducing the expression of editing targets. It is possible, however, that RNA editing by ADAR in non-coding regions of the gene might be a part of a more complex expression regulation mechanism.

Predicting protein-protein interactions in the post synaptic density.

The post synaptic density (PSD) is a specialization of the cytoskeleton at the synaptic junction, composed of hundreds of different proteins. Characterizing the protein components of the PSD and their interactions can help elucidate the mechanism of long-term changes in synaptic plasticity, which underlie learning and memory. Unfortunately, our knowledge of the proteome and interactome of the PSD is still partial and noisy. In this study we describe a computational framework to improve the reconstruction of the PSD network. The approach is based on learning the characteristics of PSD protein interactions from a set of trusted interactions, expanding this set with data collected from large scale repositories, and then predicting novel interaction with proteins that are suspected to reside in the PSD. Using this method we obtained thirty predicted interactions, with more than half of which having supporting evidence in the literature. We discuss in details two of these new interactions, Lrrtm1 with PSD-95 and Src with Capg. The first may take part in a mechanism underlying glutamatergic dysfunction in schizophrenia. The second suggests an alternative mechanism to regulate dendritic spines maturation.

A Bayesian approach for characterizing direction tuning curves in the supplementary motor area of behaving monkeys.

Neural responses are commonly studied in terms of "tuning curves," characterizing changes in neuronal response as a function of a continuous stimulus parameter. In the motor system, neural responses to movement direction often follow a bell-shaped tuning curve for which the exact shape determines the properties of neuronal movement coding. Estimating the shape of that tuning curve robustly is hard, especially when directions are sampled unevenly and at a coarse resolution. Here, we describe a Bayesian estimation procedure that improves the accuracy of curve-shape estimation even when the curve is sampled unevenly and at a very coarse resolution. Using this approach, we characterize the movement direction tuning curves in the supplementary motor area (SMA) of behaving monkeys. We compare the SMA tuning curves to tuning curves of neurons from the primary motor cortex (M1) of the same monkeys, showing that the tuning curves of the SMA neurons tend to be narrower and shallower. We also show that these characteristics do not depend on the specific location in each region.

Localizing genes to cerebellar layers by classifying ISH images.

Gene expression controls how the brain develops and functions. Understanding control processes in the brain is particularly hard since they involve numerous types of neurons and glia, and very little is known about which genes are expressed in which cells and brain layers. Here we describe an approach to detect genes whose expression is primarily localized to a specific brain layer and apply it to the mouse cerebellum. We learn typical spatial patterns of expression from a few markers that are known to be localized to specific layers, and use these patterns to predict localization for new genes. We analyze images of in-situ hybridization (ISH) experiments, which we represent using histograms of local binary patterns (LBP) and train image classifiers and gene classifiers for four layers of the cerebellum: the Purkinje, granular, molecular and white matter layer. On held-out data, the layer classifiers achieve accuracy above 94% (AUC) by representing each image at multiple scales and by combining multiple image scores into a single gene-level decision. When applied to the full mouse genome, the classifiers predict specific layer localization for hundreds of new genes in the Purkinje and granular layers. Many genes localized to the Purkinje layer are likely to be expressed in astrocytes, and many others are involved in lipid metabolism, possibly due to the unusual size of Purkinje cells.

Reduction of information redundancy in the ascending auditory pathway.

Information processing by a sensory system is reflected in the changes in stimulus representation along its successive processing stages. We measured information content and stimulus-induced redundancy in the neural responses to a set of natural sounds in three successive stations of the auditory pathway-inferior colliculus (IC), auditory thalamus (MGB), and primary auditory cortex (A1). Information about stimulus identity was somewhat reduced in single A1 and MGB neurons relative to single IC neurons, when information is measured using spike counts, latency, or temporal spiking patterns. However, most of this difference was due to differences in firing rates. On the other hand, IC neurons were substantially more redundant than A1 and MGB neurons. IC redundancy was largely related to frequency selectivity. Redundancy reduction may be a generic organization principle of neural systems, allowing for easier readout of the identity of complex stimuli in A1 relative to IC.

Sound retrieval and ranking using sparse auditory representations.

To create systems that understand the sounds that humans are exposed to in everyday life, we need to represent sounds with features that can discriminate among many different sound classes. Here, we use a sound-ranking framework to quantitatively evaluate such representations in a large-scale task. We have adapted a machine-vision method, the passive-aggressive model for image retrieval (PAMIR), which efficiently learns a linear mapping from a very large sparse feature space to a large query-term space. Using this approach, we compare different auditory front ends and different ways of extracting sparse features from high-dimensional auditory images. We tested auditory models that use an adaptive pole-zero filter cascade (PZFC) auditory filter bank and sparse-code feature extraction from stabilized auditory images with multiple vector quantizers. In addition to auditory image models, we compare a family of more conventional mel-frequency cepstral coefficient (MFCC) front ends. The experimental results show a significant advantage for the auditory models over vector-quantized MFCCs. When thousands of sound files with a query vocabulary of thousands of words were ranked, the best precision at top-1 was 73% and the average precision was 35%, reflecting a 18% improvement over the best competing MFCC front end.

Information theory in auditory research.

Mutual information (MI) is in increasing use as a way of quantifying neural responses. However, it is still considered with some doubts by many researchers, because it is not always clear what MI really measures, and because MI is hard to calculate in practice. This paper aims to clarify these issues. First, it provides an interpretation of mutual information as variability decomposition, similar to standard variance decomposition routinely used in statistical evaluations of neural data, except that the measure of variability is entropy rather than variance. Second, it discusses those aspects of the MI that makes its calculation difficult. The goal of this paper is to clarify when and how information theory can be used informatively and reliably in auditory neuroscience.

Invariant Temporal Dynamics Underlie Perceptual Stability in Human Visual Cortex.

An inherent limitation of human visual system research stems from its reliance on highly controlled laboratory conditions. Visual processing in the real world differs substantially from such controlled conditions. In particular, during natural vision, we continuously sample the dynamic environment by variable eye movements that lead to inherent instability of the optical image. The neuronal mechanism by which human perception remains stable under these natural conditions remains unknown. Here, we examined a neural mechanism that may contribute to such stability, i.e., the extent to which neuronal responses remain invariant to oculomotor parameters and viewing conditions. To this end, we introduce an experimental paradigm in which intracranial brain activity, a video of the real-life visual scene, and free oculomotor behavior were simultaneously recorded in human patients. Our results reveal, in high-order visual areas, a remarkable level of neural invariance to the length of eye fixations and lack of evidence for a saccade-related neuronal signature. Thus, neuronal responses, while showing high selectivity to the category of visual images, manifested stable "iconic" dynamics. This property of invariance to fixation onset and duration emerged only in high-order visual representations. In early visual cortex, the fixation onset was accompanied with suppressive neural signal, and duration of neuronal responses was largely determined by the fixation times. These results uncover unique neuronal dynamics in high-order ventral stream visual areas that could play an important role in achieving perceptual stability, despite the drastic changes introduced by oculomotor behavior in real life.

Discrete profile comparison using information bottleneck.

Sequence homologs are an important source of information about proteins. Amino acid profiles, representing the position-specific mutation probabilities found in profiles, are a richer encoding of biological sequences than the individual sequences themselves. However, profile comparisons are an order of magnitude slower than sequence comparisons, making profiles impractical for large datasets. Also, because they are such a rich representation, profiles are difficult to visualize. To address these problems, we describe a method to map probabilistic profiles to a discrete alphabet while preserving most of the information in the profiles. We find an informationally optimal discretization using the Information Bottleneck approach (IB). We observe that an 80-character IB alphabet captures nearly 90% of the amino acid occurrence information found in profiles, compared to the consensus sequence's 78%. Distant homolog search with IB sequences is 88% as sensitive as with profiles compared to 61% with consensus sequences (AUC scores 0.73, 0.83, and 0.51, respectively), but like simple sequence comparison, is 30 times faster. Discrete IB encoding can therefore expand the range of sequence problems to which profile information can be applied to include batch queries over large databases like SwissProt, which were previously computationally infeasible.

Learning to classify neural activity from a mouse model of Alzheimer's disease amyloidosis versus controls.

The mechanisms underlying Alzheimer's disease (AD) onset and progression are not yet elucidated. The extent to which alterations in the activity of individual neurons of an AD model are significant, and the phase at which they can be captured, point to the intensity of the pathology and imply the stage at which it can be detected. Using a machine-learning algorithm, we present a successful cell-by-cell classification of intracellularly recorded neurons from the B6C3 APPswe/PS1dE9 AD model, versus wildtypes controls, at both a late stage and at an early stage, when the plaque pathology and behavioral deficits are absent or rare. These results suggest that the deficits present in neuronal networks of both old and young transgenic animals are large enough to be apparent at the level of individual neurons, and that the pathology could be detected in nearly any given sample, even before pathologic signs.

Amyloid-ß disrupts ongoing spontaneous activity in sensory cortex.

UNLABELLED: The effect of Alzheimer's disease pathology on activity of individual neocortical neurons in the intact neural network remains obscure. Ongoing spontaneous activity, which constitutes most of neocortical activity, is the background template on which further evoked-activity is superimposed. We compared in vivo intracellular recordings and local field potentials (LFP) of ongoing activity in the barrel cortex of APP/PS1 transgenic mice and age-matched littermate CONTROLS, following significant amyloid-ß (Aß) accumulation and aggregation. We found that membrane potential dynamics of neurons in Aß-burdened cortex significantly differed from those of nontransgenic CONTROLS: durations of the depolarized state were considerably shorter, and transitions to that state frequently failed. The spiking properties of APP/PS1 neurons showed alterations from those of CONTROLS: both firing patterns and spike shape were changed in the APP/PS1 group. At the population level, LFP recordings indicated reduced coherence within neuronal assemblies of APP/PS1 mice. In addition to the physiological effects, we show that morphology of neurites within the barrel cortex of the APP/PS1 model is altered compared to CONTROLS. These results are consistent with a process where the effect of Aß on spontaneous activity of individual neurons amplifies into a network effect, reducing network integrity and leading to a wide cortical dysfunction.

Applying an artificial neural network to warfarin maintenance dose prediction.

BACKGROUND: Oral anticoagulation with warfarin can lead to life-threatening events as a result of either over-anticoagulation or undertreatment. One of the main contributors to an undesirable warfarin effect is the need to adjust its daily dose for a specific patient. The dose is adjusted empirically based on the experience of the clinician, a method that is often imprecise. There is currently no other well-accepted method for predicting the maintenance dose of warfarin. OBJECTIVE: To describe the application of an artificial neural network to the problem of warfarin maintenance dose prediction. METHODS: We designed a neural network that predicts the maintenance dose of warfarin. Data on 148 patients attending a large anticoagulant clinic were collected by file review. Using correlational analysis of the patients' data we selected the best input variables. The network was trained by using the back-propagation algorithm on a subset of our data and the results were validated against the rest of the data. We used a multivariate linear regression to create a comparable model. RESULTS: The neural network generated reasonable predictions of the maintenance dose (r = 0.823). The results of the linear regression model were similar (r = 0.800). CONCLUSION: Neural networks can be applied successfully for warfarin maintenance dose prediction. The results are promising, but further investigation is needed.

Transitions in the transcriptome of the serotonergic and dopaminergic systems in the human brain during adolescence.

Adolescence is a period of profound neurophysiological, behavioral, cognitive and psychological changes, but not much is known about the underlying molecular neural mechanisms. The aim of this study was to systematically analyze expression levels of the genes forming serotonergic and dopaminergic synapses during adolescence. We analyzed the mRNA expression profiles of genes that code for all components of serotonergic and dopaminergic synapses, in 16 brain areas from human and non-human primates from public domain databases, to detect genes whose expression changes during adolescence. Two serotonin receptors, HTR1E and HTR1B had expression levels that exhibit a sharp transition in the prefrontal cortex in adolescence, but we found no similar transition in the dopaminergic system. A similar but smoother rise in expression levels is observed in HTR4 and HTR5A, and in HTR1E and HTR1B in three other expression datasets published. An earlier rise is observed in HTR1A, and a smooth and significant rise with age is observed in the expression of HTR1E in microarray measurements in macaque monkeys. The expression of HTR1E and HTR1B is correlated across subjects within each age group, suggesting that they are controlled by common mechanisms. These results point to HTR1E and HTR1B as major candidate genes involved in adolescence maturation processes, and to their operation through common control mechanisms. The maturation profiles may also involve several other 5-HT receptors, including the genes HTR5A, HTR4 and HTR1A.