Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3748 ampR

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_3748
(Mouseover regulator name to see its description)

RSP_3748 is regulated by 21 influences and regulates 10 modules.
Regulators for RSP_3748 ampR (21)
Regulator Module Operator
RSP_0607 362 tf
RSP_0623 362 tf
RSP_1014 362 tf
RSP_1776 362 tf
RSP_2351 362 tf
RSP_2494 362 tf
RSP_2867 362 tf
RSP_2965 362 tf
RSP_3464 362 tf
RSP_0623 97 tf
RSP_1014 97 tf
RSP_1055 97 tf
RSP_1243 97 tf
RSP_1435 97 tf
RSP_1990 97 tf
RSP_2026 97 tf
RSP_2882 97 tf
RSP_2950 97 tf
RSP_3029 97 tf
RSP_3322 97 tf
RSP_3400 97 tf

Warning: RSP_3748 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
7914 1.30e-08 AgttgacatTATGtgCActcAaAT
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7915 3.90e-03 AacGcctCAaGGTTaGtCTTGCaT
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8422 1.20e-06 aAaggGcgggAccGCacagAagcg
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8423 3.10e-06 gGtgGGggCGGTCTAtccggGCc
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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_3748

RSP_3748 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_3748

RSP_3748 has total of 53 gene neighbors in modules 97, 362
Gene neighbors (53)
Gene Common Name Description Module membership
RSP_0004 RSP_0004 hypothetical protein (NCBI) 97, 303
RSP_0113 RSP_0113 Phospholipase D/Transphosphatidylase (NCBI) 176, 362
RSP_0123 cerI Autoinducer synthesis protein (NCBI) 97, 309
RSP_0318 RSP_0318 hypothetical protein (NCBI) 116, 362
RSP_0319 RSP_0319 NnrU (NCBI) 116, 362
RSP_0320 NnrT NnrT (NCBI) 116, 362
RSP_0321 norD NorD Nitric oxide reductase activation protein (NCBI) 116, 362
RSP_0322 norQ NorQ protein required for nitric oxide reductase activity (NCBI) 116, 362
RSP_0323 norB Nitric oxide reductase large subunit, cytochrome b (NCBI) 116, 362
RSP_0324 norC nitric oxide reductase subunit C, cytochrome c (NCBI) 116, 362
RSP_0325 RSP_0325 hypothetical protein (NCBI) 116, 362
RSP_0430 cobD cobalamin biosynthesis protein CobD (NCBI) 97, 171
RSP_0477 RSP_0477 hypothetical protein (NCBI) 97, 103
RSP_0572 RSP_0572 putative exonuclease (NCBI) 22, 362
RSP_0573 phoB Response regulator receiver protein (NCBI) 22, 362
RSP_0574 RSP_0574 hypothetical protein (NCBI) 22, 362
RSP_0575 RSP_0575 Predicted signal transduction protein containing cyclic nucleotide-binding and CBS domains (NCBI) 22, 362
RSP_0596 RSP_0596 Putative peptidyl-dipeptidase (NCBI) 97, 329
RSP_0606 RSP_0606 Putative redox protein (NCBI) 97, 285
RSP_0751 RSP_0751 hypothetical protein (NCBI) 62, 97
RSP_0955 RSP_0955 5'-nucleotidase (NCBI) 97, 195
RSP_1055 RSP_1055 transcriptional regulator, LysR family (NCBI) 97, 329
RSP_1348 RSP_1348 hypothetical protein (NCBI) 280, 362
RSP_1349 RSP_1349 hypothetical protein (NCBI) 160, 362
RSP_1435 RSP_1435 regulatory protein TetR family (NCBI) 62, 97
RSP_1473 RSP_1473 hypothetical protein (NCBI) 97, 244
RSP_1521 RSP_1521 hypothetical protein (NCBI) 97, 116
RSP_1824 adh Zinc-containing alcohol dehydrogenase (NCBI) 35, 97
RSP_1962 RSP_1962 hypothetical protein (NCBI) 13, 97
RSP_1990 RSP_1990 Transcriptional regulator, AsnC family (NCBI) 97, 195
RSP_2053 RSP_2053 Possible transporter, RarD family, DMT superfamily (NCBI) 73, 97
RSP_2167 RSP_2167 hypothetical protein (NCBI) 97, 262
RSP_2351 RSP_2351 hypothetical protein (NCBI) 74, 362
RSP_2357 RSP_2357 hypothetical protein (NCBI) 288, 362
RSP_2376 kbl 2-amino-3-ketobutyrate CoA ligase (NCBI) 97, 239
RSP_2641 RSP_2641 hypothetical protein (NCBI) 97, 237
RSP_2676 RSP_2676 hypothetical protein (NCBI) 73, 362
RSP_2932 hutC Histidine utilization repressor, gntR family (NCBI) 95, 97
RSP_2933 hutF Formiminoglutamate deiminase (NCBI) 95, 97
RSP_2934 hutI Imidazolone-5-propionate hydrolase (NCBI) 95, 97
RSP_2935 hutH Probable histidine ammonia-lyase (NCBI) 95, 97
RSP_2936 hutU Urocanase (NCBI) 95, 97
RSP_3029 RSP_3029 transcriptional regulator, GntR family (NCBI) 97, 157
RSP_3031 RSP_3031 ABC peptide/opine transporter, inner membrane subunit (NCBI) 97, 157
RSP_3052 RSP_3052 transcriptional regulator, LysR family (NCBI) 97, 176
RSP_3053 RSP_3053 Possible dioxygenase/glyoxalase family protein (NCBI) 97, 176
RSP_3087 dgkA diacylglycerol kinase (NCBI) 97, 176
RSP_3180 RSP_3180 Transglutaminase-like enzyme (NCBI) 38, 97
RSP_3249 RSP_3249 ABC peptide transporter, duplicated ATPase domains (NCBI) 267, 362
RSP_3251 RSP_3251 ABC peptide transporter, inner membrane subunit (NCBI) 267, 362
RSP_3400 RSP_3400 transcriptional regulator, LysR family (NCBI) 19, 97
RSP_3748 ampR transcriptional regulator, LysR family (NCBI) 97, 362
RSP_3749 ampC putative beta-lactamase precursor (NCBI) 279, 362
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_3748
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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