Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2123

Radical SAM domain protein (NCBI)

CircVis
Functional Annotations (4)
Function System
DNA repair photolyase cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2123
(Mouseover regulator name to see its description)

RSP_2123 is regulated by 25 influences and regulates 0 modules.
Regulators for RSP_2123 (25)
Regulator Module Operator
RSP_1014 73 tf
RSP_1220 73 tf
RSP_1776 73 tf
RSP_1785 73 tf
RSP_1790 73 tf
RSP_1871 73 tf
RSP_2533 73 tf
RSP_2610 73 tf
RSP_2681 73 tf
RSP_2889 73 tf
RSP_2950 73 tf
RSP_2965 73 tf
RSP_3024 73 tf
RSP_3322 73 tf
RSP_3464 73 tf
RSP_3748 73 tf
RSP_1014 244 tf
RSP_1776 244 tf
RSP_1790 244 tf
RSP_2610 244 tf
RSP_2867 244 tf
RSP_3203 244 tf
RSP_3322 244 tf
RSP_3464 244 tf
RSP_3684 244 tf

Warning: RSP_2123 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
7866 4.30e+04 aTcAcGccGCcttAttcgGtGaa
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7867 5.80e+04 ATGTCGaAAACCGA
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8206 5.50e+01 tcttgggaAaGAaa
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8207 3.30e+02 AGAtcggctg.cCGA
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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_2123

RSP_2123 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
DNA repair photolyase cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
Module neighborhood information for RSP_2123

RSP_2123 has total of 49 gene neighbors in modules 73, 244
Gene neighbors (49)
Gene Common Name Description Module membership
RSP_0088 RSP_0088 ycfI, putative structural proteins (NCBI) 73, 168
RSP_0133 RSP_0133 Na+/H+ antiporter, NhaC family (NCBI) 73, 196
RSP_0187 RSP_0187 Dihydroorotate dehydrogenase (NCBI) 83, 244
RSP_0361 sda probable L-serine dehydratase protein (NCBI) 150, 244
RSP_0498 hupC Ni, Fe hydrogenase I cytochrome b subunit (NCBI) 244, 300
RSP_0542 RSP_0542 hypothetical protein (NCBI) 244, 300
RSP_0543 fixU hypothetical protein (NCBI) 141, 244
RSP_0564 RSP_0564 hypothetical protein (NCBI) 19, 73
RSP_1210 RSP_1210 Response regulator receiver protein (NCBI) 73, 168
RSP_1319 RSP_1319 possible invasion protein (NCBI) 73, 238
RSP_1428 RSP_1428 Possible Pre (Mob) type recombination enzyme (NCBI) 73, 236
RSP_1458 RSP_1458 Putative DNA repair enzyme (NCBI) 244, 282
RSP_1473 RSP_1473 hypothetical protein (NCBI) 97, 244
RSP_1652 RSP_1652 hypothetical protein (NCBI) 73, 141
RSP_1751 RSP_1751 putative 2Fe-2S ferredoxin protein (NCBI) 244, 300
RSP_2052 RSP_2052 N6 adenine-specific DNA methyltransferase, D12 class (NCBI) 73, 379
RSP_2053 RSP_2053 Possible transporter, RarD family, DMT superfamily (NCBI) 73, 97
RSP_2056 RSP_2056 hypothetical protein (NCBI) 244, 347
RSP_2123 RSP_2123 Radical SAM domain protein (NCBI) 73, 244
RSP_2220 RSP_2220 possible flagellar motor switch protein (fliG) (NCBI) 73, 196
RSP_2383 RSP_2383 putative integral membrane protein (NCBI) 73, 150
RSP_2571 RSP_2571 putative oxidoreductase protein (NCBI) 73, 188
RSP_2675 RSP_2675 hypothetical protein (NCBI) 73, 189
RSP_2676 RSP_2676 hypothetical protein (NCBI) 73, 362
RSP_2766 RSP_2766 Uncharacterized metal-binding protein (NCBI) 73, 124
RSP_2770 RSP_2770 hypothetical protein (NCBI) 73, 238
RSP_2813 mttB putative trimethylamine methyltransferase protein (NCBI) 73, 304
RSP_2873 aglE ABC alpha-glucoside transporter, perplasmic substrate-binding protein (NCBI) 73, 307
RSP_2964 RSP_2964 hypothetical protein (NCBI) 229, 244
RSP_3024 RSP_3024 transcriptional regulator, IclR family/MhpR (NCBI) 68, 73
RSP_3129 RSP_3129 serine/threonine protein kinase (NCBI) 244, 249
RSP_3130 RSP_3130 Putative serine protease (NCBI) 83, 244
RSP_3131 RSP_3131 ABC (antimicrobial peptide) transporter, ATPase subunit (NCBI) 244, 249
RSP_3132 RSP_3132 hypothetical protein (NCBI) 244, 249
RSP_3133 RSP_3133 hypothetical protein (NCBI) 244, 249
RSP_3134 RSP_3134 Serine/threonine protein kinase (NCBI) 244, 249
RSP_3135 RSP_3135 ppkA-related protein (NCBI) 244, 292
RSP_3188 RSP_3188 ApbE family protein (NCBI) 244, 300
RSP_3190 RSP_3190 2Fe-2S ferredoxin (NCBI) 68, 244
RSP_3191 fprA Flavodoxin (NCBI) 244, 300
RSP_3199 RSP_3199 hypothetical protein (NCBI) 244, 300
RSP_3211 cbiO ABC cobalt transporter, ATPase subunit, CbiO (NCBI) 23, 244
RSP_3404 RSP_3404 hypothetical protein (NCBI) 95, 244
RSP_3405 gntR transcriptional regulator, GntR family (NCBI) 95, 244
RSP_3542 RSP_3542 hypothetical protein (NCBI) 73, 189
RSP_3627 RSP_3627 Periplasmic serine proteases (NCBI) 73, 379
RSP_3628 RSP_3628 hypothetical protein (NCBI) 150, 244
RSP_3631 RSP_3631 hypothetical protein (NCBI) 73, 253
RSP_3793 RSP_3793 hypothetical protein (NCBI) 73, 168
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_2123
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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