Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3616

transcriptional regulator, Crp-Fnr family (NCBI)

CircVis
Functional Annotations (4)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3616
(Mouseover regulator name to see its description)

RSP_3616 is regulated by 19 influences and regulates 16 modules.
Regulators for RSP_3616 (19)
Regulator Module Operator
RSP_0607 147 tf
RSP_0755 147 tf
RSP_1231 147 tf
RSP_1776 147 tf
RSP_2494 147 tf
RSP_2965 147 tf
RSP_3022 147 tf
RSP_3179 147 tf
RSP_3203 147 tf
RSP_3464 147 tf
RSP_3616 147 tf
RSP_0728 140 tf
RSP_0927 140 tf
RSP_1163 140 tf
RSP_1231 140 tf
RSP_1936 140 tf
RSP_3125 140 tf
RSP_3616 140 tf
RSP_3620 140 tf

Warning: RSP_3616 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
8000 1.50e+03 GaA.tttTaTTGC
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8001 2.40e+03 AtcTTCa
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8014 2.20e-01 GatGcGGTTCt
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8015 4.50e-01 tGGctTaACaaccGGTTA
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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_3616

RSP_3616 is enriched for 4 functions in 3 categories.
Module neighborhood information for RSP_3616

RSP_3616 has total of 36 gene neighbors in modules 140, 147
Gene neighbors (36)
Gene Common Name Description Module membership
RSP_0136 RSP_0136 putative integrase for prophage CP-933U (NCBI) 29, 140
RSP_0157 RSP_0157 Beta-mannanase (NCBI) 147, 290
RSP_0158 RSP_0158 cellulose synthase-like protein (NCBI) 147, 290
RSP_0159 galE-2 UDP-glucose 4-epimerase (NCBI) 147, 290
RSP_0160 RSP_0160 NAD-dependent epimerase/dehydratase family protein (NCBI) 147, 290
RSP_0300 RSP_0300 ABC branched chain amino acid transporter, inner membrane subunit (NCBI) 103, 147
RSP_0350 RSP_0350 hypothetical protein (NCBI) 140, 213
RSP_0533 nifQ putative nitrogen fixation protein nifQ (NCBI) 140, 313
RSP_0534 RSP_0534 putative dimeric ferredoxin (FdIII) (NCBI) 140, 313
RSP_0939 RSP_0939 hypothetical protein (NCBI) 140, 356
RSP_1309 fliP Type III secretion system inner membrane P protein (NCBI) 147, 290
RSP_1310 RSP_1310 hypothetical protein (NCBI) 147, 290
RSP_1311 fliH putative flagellar biosynthesis/type III secretory pathway protein (NCBI) 147, 290
RSP_1312 fliF flagellar MS-ring protein (RefSeq) 147, 290
RSP_1313 RSP_1313 possible flagellar synthesis protein (NCBI) 147, 290
RSP_1314 RSP_1314 hypothetical protein (NCBI) 147, 290
RSP_1315 RSP_1315 hypothetical protein (NCBI) 147, 290
RSP_1316 motA Flagellar motor protein MotA (NCBI) 147, 290
RSP_1318 RSP_1318 hypothetical protein (NCBI) 147, 325
RSP_1471 RSP_1471 hypothetical protein (NCBI) 140, 229
RSP_1679 RSP_1679 acyl-CoA dehydrogenase (NCBI) 64, 140
RSP_1964 RSP_1964 hypothetical protein (NCBI) 94, 147
RSP_2037 RSP_2037 hypothetical protein (NCBI) 138, 147
RSP_2244 RSP_2244 hypothetical protein (NCBI) 140, 325
RSP_2305 RSP_2305 MaoC family protein (NCBI) 56, 140
RSP_3337 RSP_3337 ABC spermidine/putrescine transporter, periplasmic binding protein (NCBI) 140, 183
RSP_3466 RSP_3466 hypothetical protein (NCBI) 147, 176
RSP_3467 RSP_3467 hypothetical protein (NCBI) 147, 176
RSP_3468 RSP_3468 hypothetical protein (NCBI) 147, 176
RSP_3469 RSP_3469 hypothetical protein (NCBI) 147, 176
RSP_3470 RSP_3470 hypothetical protein (NCBI) 147, 176
RSP_3471 RSP_3471 hypothetical protein (NCBI) 147, 292
RSP_3608 RSP_3608 hypothetical protein (NCBI) 147, 238
RSP_3616 RSP_3616 transcriptional regulator, Crp-Fnr family (NCBI) 140, 147
RSP_3620 RSP_3620 Cold-shock DNA-binding protein (NCBI) 56, 140
RSP_3780 RSP_3780 hypothetical protein (NCBI) 147, 292
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_3616
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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