Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2027

transcriptional regulator, LysR family (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2027
(Mouseover regulator name to see its description)

RSP_2027 is regulated by 22 influences and regulates 9 modules.
Regulators for RSP_2027 (22)
Regulator Module Operator
RSP_1014 150 tf
RSP_1518 150 tf
RSP_1776 150 tf
RSP_1790 150 tf
RSP_1867 150 tf
RSP_1871 150 tf
RSP_2533 150 tf
RSP_2800 150 tf
RSP_2853 150 tf
RSP_2867 150 tf
RSP_2922 150 tf
RSP_3024 150 tf
RSP_3203 150 tf
RSP_3322 150 tf
RSP_3464 150 tf
RSP_3684 150 tf
RSP_3700 150 tf
RSP_1231 320 tf
RSP_1518 320 tf
RSP_2494 320 tf
RSP_2853 320 tf
RSP_3464 320 tf

Warning: RSP_2027 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
8020 9.50e-09 ggcggctCctgTTgCtG..aggt
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8021 2.40e-02 AGAtGcCGaaCtaaCCCGaTTaTC
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8350 3.40e-15 aGgATTAcGGaaaa.TtAcggct.
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8351 9.10e-08 ATTgtttCgatCCTG
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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_2027

RSP_2027 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_2027

RSP_2027 has total of 45 gene neighbors in modules 150, 320
Gene neighbors (45)
Gene Common Name Description Module membership
RSP_0360 RSP_0360 hypothetical protein (NCBI) 150, 249
RSP_0361 sda probable L-serine dehydratase protein (NCBI) 150, 244
RSP_0362 RSP_0362 hypothetical protein (NCBI) 38, 320
RSP_0857 btaB S-adenosylmethionine-diacylgycerolhomoserine-N-methlytransferase (NCBI) 150, 191
RSP_0918 RSP_0918 hypothetical protein (NCBI) 150, 238
RSP_0919 RSP_0919 Short-chain dehydrogenase/reductase SDR (NCBI) 137, 150
RSP_0946 RSP_0946 putative DNA topoisomerase I protein (NCBI) 74, 150
RSP_1171 radC DNA repair protein (NCBI) 138, 150
RSP_1195 comF Competence protein F (NCBI) 74, 150
RSP_1333 RSP_1333 hypothetical protein (NCBI) 320, 342
RSP_1334 RSP_1334 possible chemotactic signal-response protein CheL (NCBI) 320, 342
RSP_1335 RSP_1335 hypothetical protein (NCBI) 320, 342
RSP_1336 RSP_1336 Possible FlgD protein (NCBI) 320, 342
RSP_1436 RSP_1436 ABC transporter, duplicated ATPase domains (NCBI) 150, 379
RSP_1796 sodC Putative Copper/Zinc superoxide dismutase (NCBI) 150, 229
RSP_1848 RSP_1848 Pyruvate kinase (NCBI) 150, 191
RSP_2021 shp Mono-heme class I cytochrome c (NCBI) 150, 229
RSP_2027 RSP_2027 transcriptional regulator, LysR family (NCBI) 150, 320
RSP_2028 RSP_2028 hypothetical protein (NCBI) 150, 191
RSP_2029 ucpA Short-chain dehydrogenase/reductase (NCBI) 150, 320
RSP_2041 RSP_2041 hypothetical protein (NCBI) 150, 191
RSP_2383 RSP_2383 putative integral membrane protein (NCBI) 73, 150
RSP_2441 tlpS Putative transducer like protein (NCBI) 304, 320
RSP_2442 mcpB Methyl accepting chemotaxis protein, McpB (NCBI) 150, 320
RSP_2443 cheY5 putative Chemotaxis response regulator, CheY5 (NCBI) 40, 320
RSP_2444 RSP_2444 hypothetical protein (NCBI) 40, 320
RSP_2445 RSP_2445 putative Alpha amylase (NCBI) 40, 320
RSP_2446 RSP_2446 Putative trehalose synthase (NCBI) 40, 320
RSP_2448 glgB1 1,4-alpha-glucan branching enzyme (Glycogen branching enzyme) (NCBI) 40, 320
RSP_2449 RSP_2449 Putative glycosyl hydrolase (NCBI) 40, 320
RSP_2450 RSP_2450 putative Alpha-amylase (NCBI) 40, 320
RSP_2451 RSP_2451 putative 4-alpha-glucanotransferase (NCBI) 40, 320
RSP_2452 RSP_2452 Alpha amylase, catalytic domain/subdomain (NCBI) 40, 320
RSP_2474 RSP_2474 hypothetical protein (NCBI) 189, 320
RSP_2479 RSP_2479 putative phage host specificity protein (NCBI) 235, 320
RSP_2570 pfpI protease I (NCBI) 124, 150
RSP_3065 RSP_3065 Putative transporter, Major facilitator superfamily (MFS) (NCBI) 77, 320
RSP_3285 iolE possible sugar phosphate isomerases/epimerases, IolE (NCBI) 150, 246
RSP_3353 RSP_3353 Phage related tail protein (NCBI) 74, 150
RSP_3614 RSP_3614 hypothetical protein (NCBI) 150, 238
RSP_3628 RSP_3628 hypothetical protein (NCBI) 150, 244
RSP_3762 RSP_3762 patch repair protein (NCBI) 150, 220
RSP_3767 RSP_3767 hypothetical protein (NCBI) 31, 150
RSP_3781 RSP_3781 putative phage terminase large subunit (NCBI) 150, 342
RSP_3782 RSP_3782 hypothetical protein (NCBI) 150, 191
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_2027
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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