Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1489

Protein containing thioredoxin domain (NCBI)

CircVis
Functional Annotations (7)
Function System
Thioredoxin domain-containing protein cog/ cog
binding go/ molecular_function
glycerol ether metabolic process go/ biological_process
electron carrier activity go/ molecular_function
protein disulfide oxidoreductase activity go/ molecular_function
cell redox homeostasis go/ biological_process
thioredoxin tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1489
(Mouseover regulator name to see its description)

RSP_1489 is regulated by 19 influences and regulates 0 modules.
Regulators for RSP_1489 (19)
Regulator Module Operator
RSP_0402 71 tf
RSP_0728 71 tf
RSP_0958 71 tf
RSP_1077 71 tf
RSP_1163 71 tf
RSP_1231 71 tf
RSP_1272 71 tf
RSP_1274 71 tf
RSP_1890 71 tf
RSP_1925 71 tf
RSP_2130 71 tf
RSP_2236 71 tf
RSP_2610 71 tf
RSP_2801 71 tf
RSP_2922 71 tf
RSP_3238 71 tf
RSP_3528 71 tf
RSP_1231 30 tf
RSP_2346 30 tf

Warning: RSP_1489 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
7780 7.00e-02 ct.TtCtCctcaTc.c
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7781 1.10e+03 CccgcaAAgggcAAgAgcaTtc
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7862 1.80e+00 aAGGGctaagtCaAtTTgGAgcAt
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7863 4.80e+03 CctTtgCCaGa
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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_1489

RSP_1489 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Thioredoxin domain-containing protein cog/ cog
binding go/ molecular_function
glycerol ether metabolic process go/ biological_process
electron carrier activity go/ molecular_function
protein disulfide oxidoreductase activity go/ molecular_function
cell redox homeostasis go/ biological_process
thioredoxin tigr/ tigrfam
Module neighborhood information for RSP_1489

RSP_1489 has total of 46 gene neighbors in modules 30, 71
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0353 RSP_0353 None 30, 297
RSP_0452 recA Recombinase A, DNA recombination protein (NCBI) 30, 93
RSP_0549 RSP_0549 hypothetical protein (NCBI) 71, 171
RSP_0657 RSP_0657 hypothetical protein (NCBI) 30, 72
RSP_0658 RSP_0658 Probable ATP-dependent helicase (NCBI) 30, 72
RSP_0659 RSP_0659 Putative metallo-phosphoesterase (NCBI) 30, 72
RSP_0769 RSP_0769 Glutathione S-transferase (NCBI) 23, 71
RSP_0823 SHMT serine hydroxymethyltransferase protein (NCBI) 71, 85
RSP_0863 leuC 3-isopropylmalate dehydratase large subunit (NCBI) 30, 203
RSP_0885 SseA Thiosulfate sulfurtransferase, Rhodanese-like (NCBI) 71, 171
RSP_0924 cinA Predicted nucleotide-utilizing enzyme/competence-damage associated protein (NCBI) 71, 286
RSP_1008 RSP_1008 4-hydroxybenzoate octaprenyltransferase (NCBI) 71, 164
RSP_1009 RSP_1009 possible outer membrane protein, OmpA family (NCBI) 71, 164
RSP_1033 RSP_1033 OmpA family protein (NCBI) 16, 71
RSP_1360 RSP_1360 hypothetical protein (NCBI) 30, 93
RSP_1410 RSP_1410 hypothetical protein (NCBI) 2, 30
RSP_1460 RSP_1460 hypothetical protein (NCBI) 71, 93
RSP_1489 RSP_1489 Protein containing thioredoxin domain (NCBI) 30, 71
RSP_1760 RSP_1760 hypothetical protein (NCBI) 71, 377
RSP_1808 trpS tryptophanyl-tRNA synthetase (NCBI) 71, 360
RSP_1843 ftsY Signal recognition particle-docking protein FtsY (NCBI) 71, 309
RSP_1851 metZ O-succinylhomoserine sulfhydrylase (NCBI) 71, 360
RSP_1997 lexA LexA repressor (NCBI) 30, 93
RSP_1998 RSP_1998 Molybdenum cofactor biosynthesis protein A (NCBI) 30, 114
RSP_2000 RSP_2000 molybdenum cofactor biosynthesis protein C (NCBI) 30, 207
RSP_2007 RSP_2007 conservd hypothetical protein (NCBI) 64, 71
RSP_2147 cysK O-acetylserine (Thiol)-lyase, cysteine synthase (NCBI) 71, 184
RSP_2193 gcvT predicted aminomethyltransferase, tetrahydrofolate dependent (NCBI) 71, 309
RSP_2336 RSP_2336 hypothetical protein (NCBI) 71, 181
RSP_2387 RSP_2387 hypothetical protein (NCBI) 71, 286
RSP_2408 RSP_2408 hypothetical protein (NCBI) 71, 322
RSP_2453 RSP_2453 putative oxidoreductase (NAD/NADP dependent) (NCBI) 71, 166
RSP_2457 RSP_2457 hypothetical protein (NCBI) 30, 267
RSP_2460 alr alanine racemase (NCBI) 30, 369
RSP_2624 RSP_2624 hypothetical protein (NCBI) 30, 93
RSP_2722 cysS Cysteinyl-tRNA synthetase, class Ia (NCBI) 30, 214
RSP_2768 RSP_2768 5-methyltetrahydrofolate S-homocysteine methyltransferase (NCBI) 27, 71
RSP_2851 RSP_2851 multidrug (bicyclomycin) efflux pump, Major facilitator superfamily (MFS) (NCBI) 12, 30
RSP_2975 RSP_2975 hypothetical protein (NCBI) 71, 309
RSP_2985 RSP_2985 hypothetical protein (NCBI) 71, 181
RSP_2986 RSP_2986 ArgE/DapE/Acy1 family protein (NCBI) 52, 71
RSP_2987 RSP_2987 probable acetyltransferase (NCBI) 71, 181
RSP_3572 galM putative aldose 1-epimerase protein (NCBI) 23, 30
RSP_3822 RSP_3822 GTP1/OBG family protein (NCBI) 30, 279
RSP_3823 proB1 glutamate 5-kinase (NCBI) 30, 240
RSP_3824 proA Gamma-glutamyl phosphate reductase GPR (NCBI) 30, 101
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_1489
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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