Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1479 OppC

ABC oligopeptide transporter, inner membrane subunit OppC (NCBI)

CircVis
Functional Annotations (5)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1479
(Mouseover regulator name to see its description)

RSP_1479 is regulated by 21 influences and regulates 0 modules.
Regulators for RSP_1479 OppC (21)
Regulator Module Operator
RSP_1607 173 tf
RSP_1871 173 tf
RSP_2610 173 tf
RSP_2800 173 tf
RSP_2867 173 tf
RSP_2963 173 tf
RSP_3238 173 tf
RSP_3322 173 tf
RSP_0071 305 tf
RSP_0547 305 tf
RSP_0611 305 tf
RSP_1191 305 tf
RSP_1243 305 tf
RSP_1486 305 tf
RSP_1892 305 tf
RSP_1952 305 tf
RSP_2410 305 tf
RSP_2888 305 tf
RSP_3238 305 tf
RSP_3341 305 tf
RSP_3616 305 tf

Warning: RSP_1479 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
8066 3.60e+00 cCgGTTAagactGCggCCgcaTGC
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8067 2.10e+01 aa.GTG.gGcAagaaccggaaAAC
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8324 4.30e-14 GAaaCCtTTgAcataGATcAA
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8325 4.50e-07 AattGATaCgcATcaAcgaa
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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_1479

RSP_1479 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
Module neighborhood information for RSP_1479

RSP_1479 has total of 36 gene neighbors in modules 173, 305
Gene neighbors (36)
Gene Common Name Description Module membership
RSP_0689 rdxS RdxS, cytochrome oxidase maturation protein, cbb3-type (NCBI) 270, 305
RSP_0690 rdxI Copper-translocating P-type ATPase, RdxI (NCBI) 270, 305
RSP_0691 rdxH RdxH (NCBI) 270, 305
RSP_0692 rdxB iron-sulfur cluster-binding protein (NCBI) 270, 305
RSP_0693 ccoP Cbb3-type cytochrome c oxidase CcoP subunit (NCBI) 270, 305
RSP_0694 ccoQ Cbb3-type cytochrome c oxidase CcoQ subunit (NCBI) 270, 305
RSP_0695 ccoO Cbb3-type cytochrome c oxidase CcoO subunit (NCBI) 270, 305
RSP_0696 ccoN Cbb3-type cytochrome oxidase CcoN subunit (NCBI) 270, 305
RSP_0697 RSP_0697 Universal stress protein (Usp) (NCBI) 305, 382
RSP_0710 dnaX DNA polymerase III tau and gamma subunits (NCBI) 173, 381
RSP_0711 YbaB hypothetical protein (NCBI) 173, 187
RSP_0712 recR recombination protein RecR (NCBI) 173, 358
RSP_0731 RSP_0731 hypothetical protein (NCBI) 173, 261
RSP_0732 RSP_0732 hypothetical protein (NCBI) 173, 261
RSP_0733 RSP_0733 cell division ATP-binding protein FtsE (NCBI) 173, 261
RSP_0734 RSP_0734 cell division protein FtsX (NCBI) 173, 261
RSP_0735 RSP_0735 Phospholipid/glycerol acyltransferase (NCBI) 173, 261
RSP_0811 RSP_0811 hypothetical protein (NCBI) 173, 207
RSP_0812 RSP_0812 Glyoxalase I (lactoylglutathione lyase) (NCBI) 108, 173
RSP_1232 RSP_1232 putative integral membrane protein (NCBI) 108, 173
RSP_1478 RSP_1478 ABC oligopeptide transporter, fused ATPase subunits (NCBI) 173, 305
RSP_1479 OppC ABC oligopeptide transporter, inner membrane subunit OppC (NCBI) 173, 305
RSP_1480 OppB ABC oligopeptide transporter, inner membrane subunit OppB (NCBI) 173, 305
RSP_1481 OppA ABC oligopeptide transporter, perplasmic substrate-binding protein OppA (NCBI) 173, 305
RSP_1592 acsA Possible acyl-CoA sythetase (NCBI) 305, 377
RSP_2394 kdtA putative 3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase) (NCBI) 305, 382
RSP_2395 RSP_2395 BCCP, cytochrome c peroxidase (NCBI) 305, 382
RSP_3585 RSP_3585 Tryptophan synthase beta chain (NCBI) 173, 182
RSP_3586 RSP_3586 Putative aromatic pathway regulator (NCBI) 36, 173
RSP_3587 RSP_3587 N-(5'-phosphoribosyl)anthranilate isomerase (NCBI) 173, 382
RSP_3640 RSP_3640 hypothetical protein (NCBI) 21, 305
RSP_3641 RSP_3641 possible pfkB family carbohydrate kinase (NCBI) 21, 305
RSP_3642 exsB putative ExsB (NCBI) 21, 305
RSP_3643 RSP_3643 hypothetical protein (NCBI) 21, 305
RSP_4355 RSP_4355 hypothetical protein (NCBI) 24, 173
RSP_6169 RSP_6169 hypothetical protein (NCBI) 123, 305
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_1479
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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