Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_4304

tRNA-Thr (NCBI)

CircVis
Functional Annotations (1)
Function System
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_4304
(Mouseover regulator name to see its description)

RSP_4304 is regulated by 11 influences and regulates 0 modules.
Regulators for RSP_4304 (11)
Regulator Module Operator
RSP_0591 225 tf
RSP_1741 225 tf
RSP_1776 225 tf
RSP_1952 225 tf
RSP_2494 225 tf
RSP_3026 225 tf
RSP_0591 336 tf
RSP_1741 336 tf
RSP_1952 336 tf
RSP_2494 336 tf
RSP_3026 336 tf

Warning: RSP_4304 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
8168 4.00e-38 cCaaCTGAGCTAc
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8169 3.70e-08 agaaatcg.cagattgcCtCTTGc
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8374 4.50e-39 cCaaCTGAGCTAc
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8375 2.60e-02 gaaatctgcagAttg.CtCTTGac
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for RSP_4304

RSP_4304 is enriched for 1 functions in 4 categories.
Enrichment Table (1)
Function System
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Module neighborhood information for RSP_4304

RSP_4304 has total of 30 gene neighbors in modules 225, 336
Gene neighbors (30)
Gene Common Name Description Module membership
RSP_4296 RSP_4296 tRNA-Gly (NCBI) 225, 336
RSP_4297 RSP_4297 tRNA-Arg (NCBI) 225, 336
RSP_4299 RSP_4299 tRNA-Asn (NCBI) 225, 336
RSP_4300 RSP_4300 tRNA-Ser (NCBI) 327, 336
RSP_4302 RSP_4302 tRNA-Ser (NCBI) 225, 336
RSP_4303 RSP_4303 tRNA-Met (NCBI) 225, 336
RSP_4304 RSP_4304 tRNA-Thr (NCBI) 225, 336
RSP_4305 RSP_4305 tRNA-Gly (NCBI) 225, 336
RSP_4306 RSP_4306 tRNA-Ser (NCBI) 75, 225
RSP_4307 RSP_4307 tRNA-Met (NCBI) 75, 225
RSP_4308 RSP_4308 tRNA-Ser (NCBI) 75, 336
RSP_4310 RSP_4310 tRNA-Arg (NCBI) 225, 336
RSP_4312 RSP_4312 tRNA-Glu (NCBI) 185, 225
RSP_4316 RSP_4316 tRNA-Asp (NCBI) 225, 336
RSP_4318 RSP_4318 tRNA-Thr (NCBI) 225, 336
RSP_4320 RSP_4320 tRNA-Arg (NCBI) 225, 336
RSP_4322 RSP_4322 tRNA-Cys (NCBI) 225, 336
RSP_4327 RSP_4327 tRNA-Gln (NCBI) 225, 336
RSP_4328 RSP_4328 tRNA-Val (NCBI) 225, 336
RSP_4329 RSP_4329 tRNA-Lys (NCBI) 225, 336
RSP_4330 RSP_4330 tRNA-Ala (NCBI) 225, 336
RSP_4331 RSP_4331 tRNA-Pro (NCBI) 181, 225
RSP_4333 RSP_4333 tRNA-Phe (NCBI) 225, 336
RSP_4334 RSP_4334 tRNA-Arg (NCBI) 225, 336
RSP_4335 RSP_4335 tRNA-Thr (NCBI) 225, 336
RSP_4336 RSP_4336 tRNA-His (NCBI) 225, 336
RSP_4337 RSP_4337 tRNA-Val (NCBI) 225, 336
RSP_4338 RSP_4338 tRNA-Leu (NCBI) 225, 336
RSP_4339 RSP_4339 tRNA-Ala (NCBI) 225, 336
RSP_4340 RSP_4340 tRNA-Tyr (NCBI) 225, 336
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for RSP_4304
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend