Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1866

Transcriptional regulator, AsnC family (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1866
(Mouseover regulator name to see its description)

RSP_1866 is regulated by 25 influences and regulates 26 modules.
Regulators for RSP_1866 (25)
Regulator Module Operator
RSP_0755 356 tf
RSP_0794 356 tf
RSP_0999 356 tf
RSP_1055 356 tf
RSP_1660 356 tf
RSP_1866 356 tf
RSP_2351 356 tf
RSP_2533 356 tf
RSP_2950 356 tf
RSP_3165 356 tf
RSP_3238 356 tf
RSP_3341 356 tf
RSP_3621 356 tf
RSP_3748 356 tf
RSP_0122 187 tf
RSP_0728 187 tf
RSP_1225 187 tf
RSP_1712 187 tf
RSP_1866 187 tf
RSP_2324 187 tf
RSP_2533 187 tf
RSP_2950 187 tf
RSP_2965 187 tf
RSP_3433 187 tf
RSP_3748 187 tf

Warning: RSP_1866 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
8094 1.80e+02 GCgAAaGt
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8095 2.80e+01 GtCaGcagctTcgAAggcaGCAG
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8410 1.70e-02 atgacacttCaGtGAaaaGA
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8411 3.80e+01 ATATCtggcAAAGGtCAT
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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_1866

RSP_1866 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for RSP_1866

RSP_1866 has total of 41 gene neighbors in modules 187, 356
Gene neighbors (41)
Gene Common Name Description Module membership
RSP_0711 YbaB hypothetical protein (NCBI) 173, 187
RSP_0736 mobC MobC protein (NCBI) 12, 187
RSP_0737 mobB Molybdopterin guanine dinucleotide synthesis (NCBI) 12, 187
RSP_0738 mobA molybdopterin-guanine dinucleotide biosynthesis protein A (NCBI) 12, 187
RSP_0821 RSP_0821 Esterase/lipase/thioesterase (NCBI) 72, 356
RSP_0877 RSP_0877 Putative transporter, RhaT family, DMT superfamily (NCBI) 29, 187
RSP_0939 RSP_0939 hypothetical protein (NCBI) 140, 356
RSP_1045 trmD tRNA (guanine-N1-)-methyltransferase (NCBI) 279, 356
RSP_1101 RSP_1101 hypothetical protein (NCBI) 129, 356
RSP_1149 gltD Glutamate synthase (beta subunit) (NCBI) 98, 356
RSP_1152 rnd Ribonuclease D (NCBI) 192, 356
RSP_1154 RSP_1154 hypothetical protein (NCBI) 129, 356
RSP_1155 RSP_1155 OstA-like protein (NCBI) 129, 356
RSP_1219 grpE putative chaperone protein GrpE (heat shock protein) (NCBI) 7, 187
RSP_1224 hemN putative Coproporphyrinogen III oxidase and related Fe-S oxidoreductases (NCBI) 68, 187
RSP_1226 RSP_1226 hypothetical protein (NCBI) 133, 187
RSP_1830 surf-1 Surf1 protein (NCBI) 126, 356
RSP_1847 PurD Phosphoribosylamine--glycine ligase (NCBI) 160, 356
RSP_1865 RSP_1865 ketol-acid reductoisomerase (NCBI) 261, 356
RSP_1866 RSP_1866 Transcriptional regulator, AsnC family (NCBI) 187, 356
RSP_1867 RSP_1867 transcriptional regulator, AsnC family (NCBI) 189, 356
RSP_2191 pccA Propionyl-CoA carboxylase alpha subunit (NCBI) 121, 356
RSP_2239 RSP_2239 tRNA/rRNA metyltransferase (NCBI) 42, 187
RSP_2284 RSP_2284 Histidinol-phosphate aminotransferase (NCBI) 311, 356
RSP_2327 RSP_2327 hypothetical protein (NCBI) 356, 383
RSP_2328 mreC Rod shape-determining protein, MreC (NCBI) 87, 356
RSP_2619 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI) 187, 356
RSP_2748 RSP_2748 possible transcriptional regulator, CopG family (NCBI) 152, 356
RSP_2790 RSP_2790 hypothetical protein (NCBI) 84, 356
RSP_2912 RSP_2912 Predicted pyrophosphatase (NCBI) 279, 356
RSP_2970 RSP_2970 Transporter, Major facilitator superfamily (MFS) (NCBI) 231, 356
RSP_3170 RSP_3170 Demethylmenaquinone methyltransferase (NCBI) 337, 356
RSP_3171 RSP_3171 3-hydroxyisobutyrate dehydrogenase (NCBI) 337, 356
RSP_3172 RSP_3172 hypothetical protein (NCBI) 337, 356
RSP_3200 RSP_3200 Molecular chaperone, DnaK (NCBI) 146, 356
RSP_3227 RSP_3227 Lysine 2,3-aminomutase (NCBI) 289, 356
RSP_3344 RSP_3344 PAS sensor diguanylate cyclase (NCBI) 174, 356
RSP_3593 RSP_3593 hypothetical protein (NCBI) 214, 356
RSP_3607 RSP_3607 hypothetical protein (NCBI) 129, 356
RSP_3729 RSP_3729 hypothetical protein (NCBI) 187, 354
RSP_3777 RSP_3777 hypothetical protein (NCBI) 29, 356
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_1866
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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