Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0623

hypothetical protein (NCBI)

CircVis
Functional Annotations (4)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0623
(Mouseover regulator name to see its description)

RSP_0623 is regulated by 31 influences and regulates 40 modules.
Regulators for RSP_0623 (31)
Regulator Module Operator
RSP_0386 263 tf
RSP_0415 263 tf
RSP_0623 263 tf
RSP_0760 263 tf
RSP_0999 263 tf
RSP_1225 263 tf
RSP_1712 263 tf
RSP_1739 263 tf
RSP_1776 263 tf
RSP_2182 263 tf
RSP_2324 263 tf
RSP_2351 263 tf
RSP_2533 263 tf
RSP_2591 263 tf
RSP_2801 263 tf
RSP_2840 263 tf
RSP_2950 263 tf
RSP_3238 263 tf
RSP_0623 65 tf
RSP_0958 65 tf
RSP_1225 65 tf
RSP_1435 65 tf
RSP_1518 65 tf
RSP_1712 65 tf
RSP_1890 65 tf
RSP_2410 65 tf
RSP_2533 65 tf
RSP_2681 65 tf
RSP_2801 65 tf
RSP_2838 65 tf
RSP_2950 65 tf

Warning: RSP_0623 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
7850 1.70e-02 att.ccTtGAA
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7851 1.40e+02 AaCCCcTtTtCaGctTctTCgAgA
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8244 5.80e-02 AtTatcccTTgAAAa
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8245 2.60e+02 GCAaAAca
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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_0623

RSP_0623 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
Module neighborhood information for RSP_0623

RSP_0623 has total of 45 gene neighbors in modules 65, 263
Gene neighbors (45)
Gene Common Name Description Module membership
RSP_0129 metN ABC D-methionine uptake transporter, ATPase subunit (NCBI) 5, 263
RSP_0132 metQ ABC D-methionine uptake transporter, substrate-binding protein (NCBI) 5, 263
RSP_0368 RSP_0368 CTP synthase (NCBI) 65, 384
RSP_0373 RSP_0373 ABC basic amino acid transporter, inner membrane subunit (NCBI) 65, 114
RSP_0374 RSP_0374 ABC basic amino acid transporter, inner membrane subunit (NCBI) 65, 114
RSP_0375 RSP_0375 probable glutamine synthetase (NCBI) 65, 67
RSP_0623 RSP_0623 hypothetical protein (NCBI) 65, 263
RSP_0624 RSP_0624 hypothetical protein (NCBI) 65, 263
RSP_0625 RSP_0625 Putative Maf-like protein (NCBI) 65, 263
RSP_0706 pheA Prephenate dehydratase (NCBI) 263, 271
RSP_0874 RSP_0874 Formylmethionine deformylase (NCBI) 47, 65
RSP_0875 fmt methionyl-tRNA formyl transferase (NCBI) 47, 65
RSP_0879 RSP_0879 hypothetical protein (NCBI) 7, 65
RSP_0970 RSP_0970 Putative citrate lyase beta chain (NCBI) 208, 263
RSP_1061 RSP_1061 hypothetical protein (NCBI) 65, 208
RSP_1132 RSP_1132 hypothetical protein (NCBI) 263, 271
RSP_1287 RSP_1287 ABC branched chain amino acid family transporter, ATPase subunit (NCBI) 215, 263
RSP_1288 RSP_1288 ABC branched chain amino acid family transporter, ATPase subunit (NCBI) 263, 383
RSP_1289 RSP_1289 ABC branched chain amino acid family transporter, inner membrane subunit (NCBI) 130, 263
RSP_1290 RSP_1290 ABC branched chain amino acid family transporter, inner membrane subunit (NCBI) 263, 383
RSP_1291 RSP_1291 ABC branched chain amino acid family transporter, periplasmic substrate binding protein (NCBI) 263, 337
RSP_1675 rnc Ribonuclease III (NCBI) 263, 383
RSP_1676 era GTP-binding protein, Era-like (NCBI) 65, 224
RSP_1874 carA Carbamoyl-phosphate synthase, small chain (NCBI) 258, 263
RSP_2042 RSP_2042 hypothetical protein (NCBI) 65, 358
RSP_2044 RSP_2044 ATPase (NCBI) 65, 358
RSP_2170 RSP_2170 Phosphate transporter, Pit family (NCBI) 263, 383
RSP_2190 RSP_2190 hypothetical protein (NCBI) 65, 130
RSP_2192 mcmA Methylmalonyl-CoA mutase (NCBI) 65, 384
RSP_2423 RSP_2423 putative Heat shock protein 15 (HSP15) (NCBI) 65, 208
RSP_2612 fabH 3-oxoacyl-(acyl-carrier-protein) synthase III (NCBI) 263, 383
RSP_2613 plsX Fatty acid/phospholipid biosynthesis enzyme (NCBI) 263, 374
RSP_2628 gltX/glnS glutamyl-/ glutaminyl-tRNA synthetase (NCBI) 65, 267
RSP_2629 gid Glucose-inhibited division protein A (NCBI) 65, 240
RSP_2918 RSP_2918 Predicted ferripyochelin binding protein (NCBI) 258, 263
RSP_2919 RSP_2919 Probable Guanylate kinase (NCBI) 258, 263
RSP_2920 RSP_2920 hypothetical protein (NCBI) 258, 263
RSP_2924 RSP_2924 ABC branched-chain amino acid transporter family, ATPase subunit (NCBI) 65, 208
RSP_2925 RSP_2925 ABC branched-chain amino acid transporter family, ATPase subunit (NCBI) 65, 208
RSP_2926 RSP_2926 ABC branched-chain amino acid transporter family, inner membrane subunit (NCBI) 65, 208
RSP_2927 RSP_2927 ABC branched-chain amino acid transporter family, inner membrane subunit (NCBI) 65, 263
RSP_2928 RSP_2928 hypothetical protein (NCBI) 65, 208
RSP_2950 RSP_2950 Transcriptional regulator, LysR family (NCBI) 7, 263
RSP_3645 RSP_3645 hypothetical protein (NCBI) 65, 130
RSP_3829 RSP_3829 tRNA/rRNA methyltransferase (SpoU) (NCBI) 263, 271
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_0623
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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