Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2578 xoxF

putative pqq dehydrogenase protein (NCBI)

CircVis
Functional Annotations (5)
Function System
Glucose dehydrogenase cog/ cog
electron transport go/ biological_process
alcohol dehydrogenase (acceptor) activity go/ molecular_function
outer membrane-bounded periplasmic space go/ cellular_component
PQQ_enz_alc_DH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2578
(Mouseover regulator name to see its description)

RSP_2578 is regulated by 18 influences and regulates 0 modules.
Regulators for RSP_2578 xoxF (18)
Regulator Module Operator
RSP_0402 26 tf
RSP_0611 26 tf
RSP_0755 26 tf
RSP_1034 26 tf
RSP_1272 26 tf
RSP_2346 26 tf
RSP_2591 26 tf
RSP_2950 26 tf
RSP_3341 26 tf
RSP_0071 364 tf
RSP_0386 364 tf
RSP_0547 364 tf
RSP_2346 364 tf
RSP_2800 364 tf
RSP_2950 364 tf
RSP_2963 364 tf
RSP_3322 364 tf
RSP_3341 364 tf

Warning: RSP_2578 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
7772 3.00e-06 AtcaTt.agcaattTT.tgccgA
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7773 3.00e-03 AtcgGgAgGA.
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8426 8.90e+02 ATgTtGAt
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8427 8.80e+03 CGGac.aG.Tc
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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_2578

RSP_2578 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Glucose dehydrogenase cog/ cog
electron transport go/ biological_process
alcohol dehydrogenase (acceptor) activity go/ molecular_function
outer membrane-bounded periplasmic space go/ cellular_component
PQQ_enz_alc_DH tigr/ tigrfam
Module neighborhood information for RSP_2578

RSP_2578 has total of 41 gene neighbors in modules 26, 364
Gene neighbors (41)
Gene Common Name Description Module membership
RSP_0402 RSP_0402 transcriptional regulator, TetR family (NCBI) 26, 259
RSP_0791 pqqD putative pyrroloquinoline quinone synthesis protein D (NCBI) 338, 364
RSP_0792 pqqC probable pyrroloquinoline quinone synthesis protein C (NCBI) 338, 364
RSP_0793 pqqB putative coenzyme PQQ synthesis protein B (NCBI) 338, 364
RSP_2161 bcrC Efflux channel (NCBI) 26, 58
RSP_2577 cycI isocytochrome c2 (NCBI) 26, 59
RSP_2578 xoxF putative pqq dehydrogenase protein (NCBI) 26, 364
RSP_2579 cycB cytochrome c553i (NCBI) 26, 364
RSP_2580 xoxJ putative methanol oxidation protein (NCBI) 26, 364
RSP_2581 RSP_2581 Rhodanese (NCBI) 26, 364
RSP_2582 RSP_2582 hypothetical protein (NCBI) 26, 363
RSP_2583 RSP_2583 hypothetical protein (NCBI) 26, 221
RSP_2585 RSP_2585 hypothetical protein (NCBI) 26, 363
RSP_2586 RSP_2586 ABC multidrug efflux transporter, ATPase subunit (NCBI) 26, 363
RSP_2587 RSP_2587 ABC multidrug efflux transporter, inner membrane subunit (NCBI) 26, 363
RSP_2591 flhR two component transcriptional regulator, LuxR family family (NCBI) 26, 363
RSP_2592 RSP_2592 hypothetical protein (NCBI) 26, 259
RSP_2593 flhS hybrid histidine kinase (NCBI) 26, 259
RSP_2594 RSP_2594 hypothetical protein (NCBI) 26, 259
RSP_2595 RSP_2595 hypothetical protein (NCBI) 26, 259
RSP_2773 RSP_2773 hypothetical protein (NCBI) 26, 48
RSP_2774 RSP_2774 hypothetical protein (NCBI) 26, 349
RSP_2817 aroK Putative shikimate kinase (NCBI) 26, 234
RSP_3369 RSP_3369 Asp-tRNA Asn/Glu-tRNA Gln amidotransferase subunit A (NCBI) 55, 364
RSP_3370 RSP_3370 TRAP-T family transporter, DctM (12 TMs) subunit (NCBI) 55, 364
RSP_3371 RSP_3371 TRAP-T family transporter, small (4 TMs) inner membrane subunit (NCBI) 55, 364
RSP_3674 RSP_3674 ABC sugar transporter, periplasmic binding protein (NCBI) 26, 115
RSP_4341 RSP_4341 None 26, 364
RSP_4342 RSP_4342 None 205, 364
RSP_6004 RSP_6004 None 284, 364
RSP_6031 RSP_6031 hypothetical protein (NCBI) 26, 165
RSP_6100 RSP_6100 None 74, 364
RSP_6160 dorY DMSO reductase regulatory protein DorY (NCBI) 266, 364
RSP_6164 RSP_6164 hypothetical protein (NCBI) 205, 364
RSP_6177 gpFI Major tail sheath protein FI (NCBI) 33, 364
RSP_6178 gpFII Putative phage tail tube protein FII (NCBI) 165, 364
RSP_6179 RSP_6179 hypothetical protein (NCBI) 266, 364
RSP_6195 RSP_6195 hypothetical protein (NCBI) 284, 364
RSP_6197 RSP_6197 hypothetical protein (NCBI) 266, 364
RSP_6217 cobH precorrin isomerase (NCBI) 266, 364
RSP_6254 RSP_6254 hypothetical protein (NCBI) 40, 364
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_2578
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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