LinkRbrain: multi-scale data integrator of the brain

Abstract

Background: LinkRbrain is an open-access web platform for multi-scale data integration and visualization of human brain data. This platform integrates anatomical, functional, and genetic knowledge produced by the scientific community.

New method: The linkRbrain platform has two major components: (1) a data aggregation component that integrates multiple open databases into a single platform with a unified representation; and (2) a website that provides fast multi-scale integration and visualization of these data and makes the results immediately available.

Results: LinkRbrain allows users to visualize functional networks or/and genetic expression over a standard brain template (MNI152). Interrelationships between these components based on topographical overlap are displayed using relational graphs. Moreover, linkRbrain enables comparison of new experimental results with previous published works.

Comparison with existing methods: Previous tools and studies illustrate the opportunities of data mining across multiple tiers of neuroscience and genetic information. However, a global systematic approach is still missing to gather cognitive, topographical, and genetic knowledge in a common framework in order to facilitate their visualization, comparison, and integration.

Conclusions: LinkRbrain is an efficient open-access tool that affords an integrative understanding of human brain function.

Keywords: Anatomo-functional; Complex systems; Genetics; Integrative; Multi-scale; Open databases; Platform.

Fig. 1

Mapping of the networks corresponding to the cognitive functions “syllables production”, “pure tone” and “lips movement” in blue, red, and green respectively. On the right side we represent the activated regions by spheres, whereas on the left side we display these networks as a continuous surface. (For interpretation of the references to color in this text, the reader is referred to the web version of the article.)

Fig. 2

3D and 2D mapping of the expression profile across the 947 brain regions for the Microtubule-associated Protein Tau (MAPT) gene. Each region is represented by a sphere whose diameter is proportional to the expression intensity at the specific region.

Fig. 3

3D and 2D mapping of the regions of maximal expression for Microtubule-associated protein tau (MAPT) and Myelin basic protein (MBP) genes. Each region is represented by a sphere colored in blue or magenta to indicate MAPT or MBP expression respectively. (For interpretation of the references to color in this text, the reader is referred to the web version of the article.)

Fig. 4

2D mapping of the cognitive network “facial expression” in green. The corresponding graph shows the neuroanatomical regions involved in this network (overlap). In the bottom, 2D mapping of the neuroanatomaical region called “Amygdala” in blue. The corresponding graph shows the sensorimotor/cognitve task-based networks that are localized in this region. (For interpretation of the references to color in this text, the reader is referred to the web version of the article.)

Fig. 5

The graph shows the topographical similarities (overlap) between “speech function” (nodes in magenta) and the 300 cognitive tasks. Only the most highly correlated tasks (25) are represented. The magenta links connect “speech” network with similar tasks. The gray links connect tasks with each others. (For interpretation of the references to color in this text, the reader is referred to the web version of the article.)

Fig. 6

Mapping of the cognitive and sensorimotor functions related to the VSA ring (in blue), and some cognitive functions that reconstruct the PTF ring (in red). The corresponding graph shows these functions and confirm the topographical similarities (overlap) between VSA/PTF (in blue/red respectively) and the 300 tasks. The blue/red links connect VSA/PTF rings (respectively) with similar tasks. The gray links connect tasks with each other. (For interpretation of the references to color in this text, the reader is referred to the web version of the article.)

Fig. 7

Mapping of the regions where the genes coding for oxytocin receptor (OXTR) and dopamine receptor D5 (DRD5) (in blue and red, respectively) are the most expressed. The regions in purple represent the overlap between the two gene expressions. The corresponding graph shows the sensorimotor/cognitives task-based networks that are localized in the same regions where the genes OXTR and DRD5 are most strongly expressed. Red links connect the DRD5 expressions with the topographically nearest tasks, whereas the blue links connect the OXTR expressions with the topographically nearest tasks. The gray links connect tasks with each other on the basis of their topographical overlaps. (For interpretation of the references to color in this text, the reader is referred to the web version of the article.)

Fig. 8

Mapping of the networks corresponding to the cognitive functions “speech” and “sentences” in purple and magenta respectively. The corresponding graph shows the topographical similarities (overlap) between the “speech” and “sentences” functions (respectively in purple and magenta) and the 300 cognitives tasks. The “purple/magenta” links connect “speech/sentences” networks (respectively) with similar tasks. The gray links connect tasks with each other. (For interpretation of the references to color in this text, the reader is referred to the web version of the article.)

Fig. 9

The graph shows the topographical similarities (overlap) between the ICN7 network (colored nodes) and the 300 cognitive tasks. The colored links connect ICN7 network with similar tasks. The gray links connect the cognitive tasks with each other. (For interpretation of the references to color in this text, the reader is referred to the web version of the article.)