Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3401

diguanylate cyclase (NCBI)

CircVis
Functional Annotations (4)
Function System
cyclic nucleotide biosynthetic process go/ biological_process
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
GGDEF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3401
(Mouseover regulator name to see its description)

RSP_3401 is regulated by 30 influences and regulates 0 modules.
Regulators for RSP_3401 (30)
Regulator Module Operator
RSP_0032 59 tf
RSP_0068 59 tf
RSP_0327 59 tf
RSP_0755 59 tf
RSP_0927 59 tf
RSP_1606 59 tf
RSP_1866 59 tf
RSP_2346 59 tf
RSP_2591 59 tf
RSP_2840 59 tf
RSP_3324 59 tf
RSP_3341 59 tf
RSP_3621 59 tf
RSP_3665 59 tf
RSP_3694 59 tf
RSP_0068 17 tf
RSP_0547 17 tf
RSP_0616 17 tf
RSP_0760 17 tf
RSP_0907 17 tf
RSP_1077 17 tf
RSP_1139 17 tf
RSP_2200 17 tf
RSP_2236 17 tf
RSP_2346 17 tf
RSP_2800 17 tf
RSP_2850 17 tf
RSP_3341 17 tf
RSP_3621 17 tf
RSP_3665 17 tf

Warning: RSP_3401 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
7754 2.10e+02 GcgGctGgaCag.g.c.aga
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7755 1.30e+03 ATGatTGTGC
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7838 2.10e+00 CtccTccctcTcgCtctcaccca
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7839 2.90e+03 TCCTcCtTGCatCc
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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_3401

RSP_3401 is enriched for 4 functions in 4 categories.
Enrichment Table (4)
Function System
cyclic nucleotide biosynthetic process go/ biological_process
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
GGDEF tigr/ tigrfam
Module neighborhood information for RSP_3401

RSP_3401 has total of 47 gene neighbors in modules 17, 59
Gene neighbors (47)
Gene Common Name Description Module membership
RSP_0334 RSP_0334 hypothetical protein (NCBI) 59, 259
RSP_0634 RSP_0634 TRAP-T family transporter, DctM (12 TMs) subunit (NCBI) 17, 141
RSP_0635 RSP_0635 TRAP-T family transporter, DctQ (4 TMs) subunit (NCBI) 17, 141
RSP_0636 RSP_0636 TRAP-T family transporter, DctP (periplasmic binding) subunit (NCBI) 17, 141
RSP_0664 RSP_0664 hypothetical protein (NCBI) 59, 344
RSP_0724 mscL Large-conductance mechanosensitive channel (NCBI) 59, 234
RSP_0760 mucS transcriptional regulator, MarR family (NCBI) 17, 214
RSP_0858 RSP_0858 Putative transporter, RhaT family, DMT superfamily (NCBI) 59, 88
RSP_1012 gabD4 succinate-semialdehyde dehdyrogenase (NCBI) 59, 344
RSP_1094 RSP_1094 hypothetical protein (NCBI) 17, 326
RSP_1186 RSP_1186 hypothetical protein (NCBI) 59, 67
RSP_1187 RSP_1187 hypothetical protein (NCBI) 7, 59
RSP_1188 wcaG Nucleotide sugar epimerase/dehydratase (NCBI) 59, 381
RSP_1451 RSP_1451 ABC peptide/nickel/opine transporter, periplasmic substrate-binding protein (NCBI) 17, 105
RSP_1452 RSP_1452 ABC peptide/nickel/opine transporter, inner membrane subunit (NCBI) 17, 59
RSP_1453 RSP_1453 ABC peptide/nickel/opine transporter, inner membrane subunit (NCBI) 17, 105
RSP_1454 RSP_1454 ABC peptide/nickel/opine transporter, fused ATPase subunits (NCBI) 17, 105
RSP_1455 RSP_1455 putative N-carbamoyl-beta-alanine amidohydrolase (NCBI) 17, 105
RSP_1457 RSP_1457 putative choline kinase (NCBI) 17, 105
RSP_1505 RSP_1505 Putative Metallo-phosphoesterase (NCBI) 59, 344
RSP_1507 RSP_1507 Aldehyde dehydrogenase (NCBI) 59, 344
RSP_2154 RSP_2154 hypothetical protein (NCBI) 17, 114
RSP_2155 hisD Histidinol dehydrogenase (NCBI) 17, 59
RSP_2158 RSP_2158 ABC transporter, periplasmic solute-binding protein (NCBI) 57, 59
RSP_2159 RSP_2159 ABC transporter, ATPase subunit (NCBI) 59, 299
RSP_2334 pfkB carbohydrate kinase, PfkB (NCBI) 59, 344
RSP_2496 RSP_2496 hypothetical protein (NCBI) 47, 59
RSP_2532 birA putative biotin protein ligase (NCBI) 17, 361
RSP_2539 RSP_2539 ABC transporter, ATPase subunit (NCBI) 17, 44
RSP_2577 cycI isocytochrome c2 (NCBI) 26, 59
RSP_2844 RSP_2844 Putative GTP-binding protein (NCBI) 59, 114
RSP_3292 RSP_3292 Glucose-methanol-choline oxidoreductase (NCBI) 17, 55
RSP_3293 RSP_3293 ABC branched-chain amino acid transporter, inner membrane subunit (NCBI) 17, 55
RSP_3294 RSP_3294 ABC branched-chain amino acid transporter, inner membrane subunit (NCBI) 17, 55
RSP_3295 RSP_3295 ABC branched-chain amino acid transporter, ATPase subunit (NCBI) 17, 55
RSP_3296 RSP_3296 ABC branched-chain amino acid transporter, ATPase subunit (NCBI) 17, 55
RSP_3297 RSP_3297 ABC branched-chain amino acid transporter, periplasmic binding protein (NCBI) 17, 55
RSP_3401 RSP_3401 diguanylate cyclase (NCBI) 17, 59
RSP_3402 RSP_3402 multisensor diguanylate cyclase/phosphodiesterase (NCBI) 17, 215
RSP_3508 RSP_3508 predicted acetamidase/formamidase (NCBI) 59, 344
RSP_3538 RSP_3538 hypothetical protein (NCBI) 59, 344
RSP_3539 RSP_3539 Hemolysin-type calcium-binding region, RTX (NCBI) 59, 344
RSP_3540 RSP_3540 Putative adhesin or RTX toxin (NCBI) 59, 344
RSP_3717 RSP_3717 hypothetical protein (NCBI) 17, 58
RSP_3718 RSP_3718 hypothetical protein (NCBI) 17, 58
RSP_3833 fadB enoyl CoA hydratase (NCBI) 59, 278
RSP_3834 RSP_3834 hypothetical protein (NCBI) 59, 274
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_3401
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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