Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2006 amsA

hypothetical protein (NCBI)

CircVis
Functional Annotations (1)
Function System
Uncharacterized protein involved in outer membrane biogenesis cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2006
(Mouseover regulator name to see its description)

RSP_2006 is regulated by 19 influences and regulates 0 modules.
Regulators for RSP_2006 amsA (19)
Regulator Module Operator
RSP_0327 329 tf
RSP_0623 329 tf
RSP_1055 329 tf
RSP_1243 329 tf
RSP_1414 329 tf
RSP_1550 329 tf
RSP_1890 329 tf
RSP_3029 329 tf
RSP_3202 329 tf
RSP_0090 92 tf
RSP_0316 92 tf
RSP_0386 92 tf
RSP_0547 92 tf
RSP_0623 92 tf
RSP_0999 92 tf
RSP_1790 92 tf
RSP_1866 92 tf
RSP_3238 92 tf
RSP_3686 92 tf

Warning: RSP_2006 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
7904 9.10e-01 T.tcgAGa.AtttaT
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7905 6.20e-02 GgcgCgCttccacCTGcCcg
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8364 1.80e+03 TTATCTTtTCATT
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8365 7.10e+03 cTCC.Tct
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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_2006

RSP_2006 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized protein involved in outer membrane biogenesis cog/ cog
Module neighborhood information for RSP_2006

RSP_2006 has total of 41 gene neighbors in modules 92, 329
Gene neighbors (41)
Gene Common Name Description Module membership
RSP_0184 RSP_0184 putative N-carbamyl-L-amino acid amidohydrolase (NCBI) 92, 102
RSP_0185 RSP_0185 Transcriptional regulator, TetR family (NCBI) 92, 102
RSP_0186 RSP_0186 Transcriptional regulator, TetR family (NCBI) 92, 370
RSP_0203 RSP_0203 signal transduction kinase protein (NCBI) 1, 329
RSP_0384 RSP_0384 hypothetical protein (NCBI) 329, 381
RSP_0429 RSP_0429 Probable ABC drug/toxin efflux transporter; fused ATPase and inner membrane subunits (NCBI) 176, 329
RSP_0491 hupT Hydrogen uptake histidine-kinase (NCBI) 308, 329
RSP_0595 RSP_0595 hypothetical protein (NCBI) 285, 329
RSP_0596 RSP_0596 Putative peptidyl-dipeptidase (NCBI) 97, 329
RSP_0643 RSP_0643 periplasmic sensor signal transduction histidine kinase (NCBI) 92, 118
RSP_0678 RSP_0678 hypothetical protein (NCBI) 23, 329
RSP_0709 cpdB 2',3'-cyclic-nucleotide 2'-phosphodiesterase (NCBI) 285, 329
RSP_0787 RSP_0787 hypothetical protein (NCBI) 41, 92
RSP_0788 RSP_0788 hypothetical protein (NCBI) 41, 92
RSP_0872 def1 Formylmethionine deformylase (NCBI) 92, 195
RSP_0881 RSP_0881 Putative soluble lytic transglycosylase (NCBI) 294, 329
RSP_0940 RSP_0940 ABC transporter, periplasmic substrate binding protein (NCBI) 92, 195
RSP_0941 RSP_0941 ABC transporter, ATPase subunit (NCBI) 92, 176
RSP_0942 RSP_0942 ABC transporter, inner membrane subunit (NCBI) 92, 176
RSP_0985 RSP_0985 adenine deaminase (NCBI) 285, 329
RSP_1055 RSP_1055 transcriptional regulator, LysR family (NCBI) 97, 329
RSP_1083 RSP_1083 two component transcriptional regulator, winged helix family (NCBI) 285, 329
RSP_1308 RSP_1308 hypothetical protein (NCBI) 92, 102
RSP_1355 RSP_1355 Glycosyl transferase, family 51 (NCBI) 92, 102
RSP_1356 RSP_1356 hypothetical protein (NCBI) 81, 92
RSP_1415 RSP_1415 putative polysaccharide deacetylase (NCBI) 23, 329
RSP_1416 RSP_1416 hypothetical protein (NCBI) 23, 329
RSP_1555 RSP_1555 Transthyretin-like protein (NCBI) 329, 381
RSP_1567 RSP_1567 Probable sensory transduction histidine kinase (NCBI) 92, 195
RSP_1844 RSP_1844 hypothetical protein (NCBI) 35, 329
RSP_2006 amsA hypothetical protein (NCBI) 92, 329
RSP_2093 RSP_2093 Putative Mrp (Multidrug resistance-associated proteins) family protein (NCBI) 278, 329
RSP_2830 RSP_2830 hypothetical protein (NCBI) 92, 139
RSP_2831 cobO Probable cob(I)alamin adenosyltransferase (NCBI) 92, 163
RSP_2869 RSP_2869 Possible tellurite resistance protein (NCBI) 329, 381
RSP_3071 RSP_3071 putative hydroxypyruvate reductase/glycerate kinase (NCBI) 107, 329
RSP_3325 RSP_3325 Polysaccharide export transporter, PST Family (NCBI) 195, 329
RSP_3326 RSP_3326 Low molecular weight phosphotyrosine protein phosphatase (NCBI) 36, 92
RSP_3342 bfr Bacterioferritin (NCBI) 92, 118
RSP_3679 RSP_3679 hypothetical protein (NCBI) 308, 329
RSP_3836 RSP_3836 Putative metal-dependent hydrolase (NCBI) 10, 329
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_2006
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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