Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1867

transcriptional regulator, AsnC family (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulators cog/ cog
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_1867
(Mouseover regulator name to see its description)

RSP_1867 is regulated by 26 influences and regulates 11 modules.
Regulators for RSP_1867 (26)
Regulator Module Operator
RSP_1077 189 tf
RSP_1220 189 tf
RSP_1607 189 tf
RSP_1660 189 tf
RSP_1776 189 tf
RSP_1867 189 tf
RSP_3001 189 tf
RSP_3064 189 tf
RSP_3179 189 tf
RSP_3418 189 tf
RSP_3464 189 tf
RSP_3684 189 tf
RSP_0755 356 tf
RSP_0794 356 tf
RSP_0999 356 tf
RSP_1055 356 tf
RSP_1660 356 tf
RSP_1866 356 tf
RSP_2351 356 tf
RSP_2533 356 tf
RSP_2950 356 tf
RSP_3165 356 tf
RSP_3238 356 tf
RSP_3341 356 tf
RSP_3621 356 tf
RSP_3748 356 tf

Warning: RSP_1867 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
8098 2.00e-03 aAtgaCctTtcgGaA
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8099 2.60e+00 CAgaAAgAAaat
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8410 1.70e-02 atgacacttCaGtGAaaaGA
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8411 3.80e+01 ATATCtggcAAAGGtCAT
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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_1867

RSP_1867 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcriptional regulators cog/ cog
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_1867

RSP_1867 has total of 53 gene neighbors in modules 189, 356
Gene neighbors (53)
Gene Common Name Description Module membership
RSP_0216 RSP_0216 hypothetical protein (NCBI) 189, 213
RSP_0226 RSP_0226 Naringenin-chalcone synthase (NCBI) 62, 189
RSP_0227 RSP_0227 hypothetical protein (NCBI) 88, 189
RSP_0821 RSP_0821 Esterase/lipase/thioesterase (NCBI) 72, 356
RSP_0939 RSP_0939 hypothetical protein (NCBI) 140, 356
RSP_1045 trmD tRNA (guanine-N1-)-methyltransferase (NCBI) 279, 356
RSP_1063 RSP_1063 Putative Cyclic-diGMP cyclase/phophodiesterase (NCBI) 19, 189
RSP_1101 RSP_1101 hypothetical protein (NCBI) 129, 356
RSP_1149 gltD Glutamate synthase (beta subunit) (NCBI) 98, 356
RSP_1152 rnd Ribonuclease D (NCBI) 192, 356
RSP_1154 RSP_1154 hypothetical protein (NCBI) 129, 356
RSP_1155 RSP_1155 OstA-like protein (NCBI) 129, 356
RSP_1378 RSP_1378 hypothetical protein (NCBI) 175, 189
RSP_1619 RSP_1619 hypothetical protein (NCBI) 189, 235
RSP_1830 surf-1 Surf1 protein (NCBI) 126, 356
RSP_1847 PurD Phosphoribosylamine--glycine ligase (NCBI) 160, 356
RSP_1865 RSP_1865 ketol-acid reductoisomerase (NCBI) 261, 356
RSP_1866 RSP_1866 Transcriptional regulator, AsnC family (NCBI) 187, 356
RSP_1867 RSP_1867 transcriptional regulator, AsnC family (NCBI) 189, 356
RSP_2076 RSP_2076 hypothetical protein (NCBI) 189, 355
RSP_2191 pccA Propionyl-CoA carboxylase alpha subunit (NCBI) 121, 356
RSP_2284 RSP_2284 Histidinol-phosphate aminotransferase (NCBI) 311, 356
RSP_2327 RSP_2327 hypothetical protein (NCBI) 356, 383
RSP_2328 mreC Rod shape-determining protein, MreC (NCBI) 87, 356
RSP_2474 RSP_2474 hypothetical protein (NCBI) 189, 320
RSP_2477 RSP_2477 hypothetical protein (NCBI) 189, 193
RSP_2619 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI) 187, 356
RSP_2675 RSP_2675 hypothetical protein (NCBI) 73, 189
RSP_2748 RSP_2748 possible transcriptional regulator, CopG family (NCBI) 152, 356
RSP_2790 RSP_2790 hypothetical protein (NCBI) 84, 356
RSP_2912 RSP_2912 Predicted pyrophosphatase (NCBI) 279, 356
RSP_2970 RSP_2970 Transporter, Major facilitator superfamily (MFS) (NCBI) 231, 356
RSP_2991 RSP_2991 hypothetical protein (NCBI) 14, 189
RSP_2998 RSP_2998 Hypothetical Terminase large subunit (NCBI) 14, 189
RSP_2999 RSP_2999 hypothetical protein (NCBI) 14, 189
RSP_3001 RSP_3001 Possible Endonuclease (NCBI) 14, 189
RSP_3170 RSP_3170 Demethylmenaquinone methyltransferase (NCBI) 337, 356
RSP_3171 RSP_3171 3-hydroxyisobutyrate dehydrogenase (NCBI) 337, 356
RSP_3172 RSP_3172 hypothetical protein (NCBI) 337, 356
RSP_3200 RSP_3200 Molecular chaperone, DnaK (NCBI) 146, 356
RSP_3227 RSP_3227 Lysine 2,3-aminomutase (NCBI) 289, 356
RSP_3344 RSP_3344 PAS sensor diguanylate cyclase (NCBI) 174, 356
RSP_3542 RSP_3542 hypothetical protein (NCBI) 73, 189
RSP_3593 RSP_3593 hypothetical protein (NCBI) 214, 356
RSP_3607 RSP_3607 hypothetical protein (NCBI) 129, 356
RSP_3651 RSP_3651 putative membrane protein (NCBI) 189, 233
RSP_3692 RSP_3692 Carbohydrate kinase, PfkB/Ribokinase (NCBI) 94, 189
RSP_3773 RSP_3773 hypothetical protein (NCBI) 189, 380
RSP_3777 RSP_3777 hypothetical protein (NCBI) 29, 356
RSP_3812 RSP_3812 recombinase (NCBI) 103, 189
RSP_3813 parB ParB-like nuclease (NCBI) 189, 288
RSP_3814 RSP_3814 hypothetical protein (NCBI) 189, 304
RSP_3816 RSP_3816 hypothetical protein (NCBI) 19, 189
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_1867
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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