Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3203

transcriptional regulator, AraC family (NCBI)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3203
(Mouseover regulator name to see its description)

RSP_3203 is regulated by 30 influences and regulates 20 modules.
Regulators for RSP_3203 (30)
Regulator Module Operator
RSP_1014 19 tf
RSP_1660 19 tf
RSP_1776 19 tf
RSP_1790 19 tf
RSP_2610 19 tf
RSP_2867 19 tf
RSP_2965 19 tf
RSP_3064 19 tf
RSP_3203 19 tf
RSP_3400 19 tf
RSP_3684 19 tf
RSP_0386 14 tf
RSP_0457 14 tf
RSP_0601 14 tf
RSP_1034 14 tf
RSP_1225 14 tf
RSP_1607 14 tf
RSP_1660 14 tf
RSP_2011 14 tf
RSP_2079 14 tf
RSP_2324 14 tf
RSP_2840 14 tf
RSP_2850 14 tf
RSP_2939 14 tf
RSP_2965 14 tf
RSP_3001 14 tf
RSP_3052 14 tf
RSP_3203 14 tf
RSP_3464 14 tf
RSP_3684 14 tf

Warning: RSP_3203 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
7748 3.00e-08 aATttAgatttacgaa.c.tt
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7749 6.30e+00 TA.ttC.acATgaCgAaTT
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7758 7.60e+01 AatcctCattaaccaaAaCTGct
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7759 4.80e+03 CcGccTTC
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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_3203

RSP_3203 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for RSP_3203

RSP_3203 has total of 51 gene neighbors in modules 14, 19
Gene neighbors (51)
Gene Common Name Description Module membership
RSP_0116 RSP_0116 hypothetical protein (NCBI) 14, 229
RSP_0221 RSP_0221 plasma membrane H+-transporting two-sector ATPase, C subunit (NCBI) 14, 342
RSP_0381 RSP_0381 hypothetical protein (NCBI) 14, 43
RSP_0564 RSP_0564 hypothetical protein (NCBI) 19, 73
RSP_0621 RSP_0621 Possible DNA helicase (NCBI) 14, 36
RSP_0945 RSP_0945 Major facilitator superfamily (MFS) transporter (NCBI) 19, 247
RSP_0961 MeaA similiar to methylmalonyl-CoA mutases (NCBI) 14, 253
RSP_1063 RSP_1063 Putative Cyclic-diGMP cyclase/phophodiesterase (NCBI) 19, 189
RSP_1966 RSP_1966 possible ISSod13, transposase (NCBI) 19, 285
RSP_2011 RSP_2011 putative transcription elongation factor (NCBI) 14, 128
RSP_2033 RSP_2033 hypothetical protein (NCBI) 19, 238
RSP_2140 RSP_2140 hypothetical protein (NCBI) 19, 38
RSP_2187 RSP_2187 multidrug efflux pump, Major Facilitator Superfamily ( MFS) (NCBI) 19, 307
RSP_2291 RSP_2291 hypothetical protein (NCBI) 14, 370
RSP_2384 RSP_2384 hypothetical protein (NCBI) 19, 368
RSP_2700 RSP_2700 ABC oligo/dipeptide transporter, fused ATPase subunits (NCBI) 19, 249
RSP_2701 RSP_2701 ABC oligo/dipeptide transporter, inner membrane subunit (NCBI) 19, 249
RSP_2702 RSP_2702 ABC oligo/dipeptide transporter, inner membrane subunit (NCBI) 19, 302
RSP_2807 RSP_2807 putative cytochrome b (NCBI) 14, 229
RSP_2808 RSP_2808 hypothetical protein (NCBI) 14, 229
RSP_2965 RSP_2965 Transcriptional regulator, LysR family (NCBI) 19, 280
RSP_2991 RSP_2991 hypothetical protein (NCBI) 14, 189
RSP_2993 RSP_2993 hypothetical protein (NCBI) 19, 355
RSP_2996 RSP_2996 putative prohead protease (NCBI) 14, 235
RSP_2997 RSP_2997 putative head portal protein (NCBI) 14, 235
RSP_2998 RSP_2998 Hypothetical Terminase large subunit (NCBI) 14, 189
RSP_2999 RSP_2999 hypothetical protein (NCBI) 14, 189
RSP_3000 RSP_3000 hypothetical protein (NCBI) 14, 325
RSP_3001 RSP_3001 Possible Endonuclease (NCBI) 14, 189
RSP_3067 RSP_3067 hypothetical protein (NCBI) 2, 19
RSP_3097 qoxA QoxA, Quinol oxidase subunit I (NCBI) 19, 380
RSP_3103 RSP_3103 hypothetical protein (NCBI) 19, 304
RSP_3119 RSP_3119 conserved hypothetical protein / putative esterase (NCBI) 14, 38
RSP_3157 RSP_3157 ABC transporter, inner membrane subunit (NCBI) 19, 176
RSP_3175 RSP_3175 hypothetical protein (NCBI) 14, 19
RSP_3203 RSP_3203 transcriptional regulator, AraC family (NCBI) 14, 19
RSP_3240 RSP_3240 periplasmic sensor signal transduction histidine kinase (NCBI) 14, 19
RSP_3252 RSP_3252 ABC peptide transporter, fused ATPase domains (NCBI) 14, 325
RSP_3264 RSP_3264 probable c-type cytochrome (NCBI) 14, 27
RSP_3312 RSP_3312 hypothetical protein (NCBI) 14, 188
RSP_3343 RSP_3343 putative glycosyl transferase (NCBI) 14, 168
RSP_3400 RSP_3400 transcriptional regulator, LysR family (NCBI) 19, 97
RSP_3428 RSP_3428 hypothetical protein (NCBI) 14, 116
RSP_3434 RSP_3434 hypothetical protein (NCBI) 14, 144
RSP_3544 RSP_3544 hypothetical protein (NCBI) 14, 342
RSP_3573 gvpA Gas vesicle protein GVPa (NCBI) 14, 27
RSP_3626 RSP_3626 None 19, 379
RSP_3753 RSP_3753 hypothetical protein (NCBI) 14, 183
RSP_3816 RSP_3816 hypothetical protein (NCBI) 19, 189
RSP_4294 RSP_4294 16S ribosomal RNA (NCBI) 14, 43
RSP_4295 RSP_4295 23S ribosomal RNA (NCBI) 14, 310
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_3203
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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