Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3179 fur

probable Ferric-uptake regulator (NCBI)

CircVis
Functional Annotations (3)
Function System
Fe2+/Zn2+ uptake regulation proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3179
(Mouseover regulator name to see its description)

RSP_3179 is regulated by 19 influences and regulates 22 modules.
Regulators for RSP_3179 fur (19)
Regulator Module Operator
RSP_0402 363 tf
RSP_0755 363 tf
RSP_1163 363 tf
RSP_1704 363 tf
RSP_2591 363 tf
RSP_3341 363 tf
RSP_0018 58 tf
RSP_0068 58 tf
RSP_0547 58 tf
RSP_0601 58 tf
RSP_0611 58 tf
RSP_1274 58 tf
RSP_1776 58 tf
RSP_1892 58 tf
RSP_2346 58 tf
RSP_2850 58 tf
RSP_2888 58 tf
RSP_3179 58 tf
RSP_3341 58 tf

Warning: RSP_3179 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
7836 6.20e-04 tGtTTTT
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7837 8.10e+01 TTCcAGAcCgAAagtTtAC
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8424 3.40e-09 AAAtTaAAactGAAaGAcCaATcT
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8425 2.40e-01 AAGcGGcTGAcccaaGGacGGAcG
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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_3179

RSP_3179 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Fe2+/Zn2+ uptake regulation proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_3179

RSP_3179 has total of 53 gene neighbors in modules 58, 363
Gene neighbors (53)
Gene Common Name Description Module membership
RSP_0099 RSP_0099 TRAP-T family sorbitol/mannitol transporter, DctQ (4TMs) subunit (NCBI) 291, 363
RSP_0165 RSP_0165 hypothetical protein (NCBI) 58, 345
RSP_0418 RSP_0418 hypothetical protein (NCBI) 58, 234
RSP_0490 RSP_0490 carbohydrate kinase (NCBI) 271, 363
RSP_0601 rpoH2 sigma factor RpoH2 (Sigma-32 group (NCBI) 58, 161
RSP_0611 RSP_0611 transcriptional regulator, ArsR family (NCBI) 58, 274
RSP_0705 RSP_0705 Cytochrome cy (NCBI) 58, 271
RSP_0899 RSP_0899 AhpC/TSA family protein (NCBI) 58, 142
RSP_0910 dctP TRAP-T family transporter, C4-dicarboxylate-binding protein DctP (NCBI) 310, 363
RSP_0911 dctQ TRAP-T family C4-dicarboxylate transporter, DctQ (4TMs) subunit (NCBI) 363, 369
RSP_0912 dctM TRAP-T family C4-dicarboxylate transporter, DctM (12TMs) subunit (NCBI) 363, 369
RSP_1041 RSP_1041 Malonyl CoA synthetase (NCBI) 214, 363
RSP_1176 xylA Xylose isomerase (NCBI) 86, 363
RSP_1177 xylB Xylulose kinase (NCBI) 86, 363
RSP_1178 RSP_1178 ABC sugar (xylose) transporter, ATPase subunit (NCBI) 86, 363
RSP_1179 xylH ABC sugar (xylose) transporter, inner membrane subunit (NCBI) 86, 363
RSP_1180 xylF ABC sugar (xylose) transporter, periplasmic binding protein (NCBI) 86, 363
RSP_1181 xylR xylose operon repressor (NCBI) 86, 363
RSP_1403 RSP_1403 conserved hypoothetical protein (NCBI) 58, 181
RSP_1599 RSP_1599 AMP-binding protein (NCBI) 350, 363
RSP_1692 pduO hypothetical protein (NCBI) 58, 231
RSP_1912 RSP_1912 hypothetical protein (NCBI) 110, 363
RSP_1913 RSP_1913 3-oxoadipate CoA-transferase, beta subunit (NCBI) 25, 363
RSP_1914 RSP_1914 3-ketoacid CoA transferase alpha subunit (NCBI) 25, 363
RSP_2082 RSP_2082 putative NADH-ubiquinone oxidoreductase-related protein (NCBI) 58, 372
RSP_2128 purQ phosphoribosylformylglycinamidine synthase I (FGAM) synthase (NCBI) 58, 231
RSP_2161 bcrC Efflux channel (NCBI) 26, 58
RSP_2228 RSP_2228 PAS domain containing protein (NCBI) 58, 353
RSP_2229 RSP_2229 Chemotaxis multidomain, CheB methylesterase/CheR, Methylase (NCBI) 58, 353
RSP_2346 RSP_2346 Cold-shock DNA-binding domain protein (NCBI) 58, 274
RSP_2347 RSP_2347 hypothetical protein (NCBI) 58, 274
RSP_2538 fabG Short-chain dehydrogenase/reductase (NCBI) 58, 274
RSP_2547 exoY exopolysaccharide production protein exoY (NCBI) 58, 349
RSP_2548 exoF Outer membrane polysaccharide export protein, exoF (NCBI) 58, 349
RSP_2582 RSP_2582 hypothetical protein (NCBI) 26, 363
RSP_2584 RSP_2584 hypothetical protein (NCBI) 221, 363
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_2588 RSP_2588 hypothetical protein (NCBI) 157, 363
RSP_2591 flhR two component transcriptional regulator, LuxR family family (NCBI) 26, 363
RSP_2961 RSP_2961 Protein containing a CBS domain (NCBI) 58, 274
RSP_2976 RSP_2976 hypothetical protein (NCBI) 58, 372
RSP_3162 RSP_3162 hypothetical protein (NCBI) 58, 231
RSP_3163 RSP_3163 Probable oxidoreductase (NCBI) 58, 231
RSP_3164 RSP_3164 ferredoxin like protein (NCBI) 58, 231
RSP_3176 fabI enoyl-(acyl-carrier protein) reductase (NADH) (NCBI) 108, 363
RSP_3177 fabB 3-oxoacyl-(Acyl-carrier-protein) synthase (NCBI) 360, 363
RSP_3178 fabA 3-hydroxydecanoyl-(acyl-carrier-protein) dehydratase (NCBI) 360, 363
RSP_3179 fur probable Ferric-uptake regulator (NCBI) 58, 363
RSP_3717 RSP_3717 hypothetical protein (NCBI) 17, 58
RSP_3718 RSP_3718 hypothetical protein (NCBI) 17, 58
RSP_3721 RSP_3721 hypothetical protein (NCBI) 58, 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_3179
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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