Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0706 pheA

Prephenate dehydratase (NCBI)

CircVis
Functional Annotations (7)
Function System
Prephenate dehydratase cog/ cog
prephenate dehydratase activity go/ molecular_function
L-phenylalanine biosynthetic process go/ biological_process
amino acid binding go/ molecular_function
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0706
(Mouseover regulator name to see its description)

RSP_0706 is regulated by 33 influences and regulates 0 modules.
Regulators for RSP_0706 pheA (33)
Regulator Module Operator
RSP_0386 263 tf
RSP_0415 263 tf
RSP_0623 263 tf
RSP_0760 263 tf
RSP_0999 263 tf
RSP_1225 263 tf
RSP_1712 263 tf
RSP_1739 263 tf
RSP_1776 263 tf
RSP_2182 263 tf
RSP_2324 263 tf
RSP_2351 263 tf
RSP_2533 263 tf
RSP_2591 263 tf
RSP_2801 263 tf
RSP_2840 263 tf
RSP_2950 263 tf
RSP_3238 263 tf
RSP_0386 271 tf
RSP_0443 271 tf
RSP_0547 271 tf
RSP_0623 271 tf
RSP_0999 271 tf
RSP_1092 271 tf
RSP_1225 271 tf
RSP_1231 271 tf
RSP_1739 271 tf
RSP_1776 271 tf
RSP_2027 271 tf
RSP_2130 271 tf
RSP_2494 271 tf
RSP_3238 271 tf
RSP_3317 271 tf

Warning: RSP_0706 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
8244 5.80e-02 AtTatcccTTgAAAa
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8245 2.60e+02 GCAaAAca
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8258 9.70e-04 CacAAgCCgaaGgat.TgC
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8259 4.50e+00 GGGaaGaAGCGGacAaAcGT
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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_0706

RSP_0706 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Prephenate dehydratase cog/ cog
prephenate dehydratase activity go/ molecular_function
L-phenylalanine biosynthetic process go/ biological_process
amino acid binding go/ molecular_function
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for RSP_0706

RSP_0706 has total of 46 gene neighbors in modules 263, 271
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0129 metN ABC D-methionine uptake transporter, ATPase subunit (NCBI) 5, 263
RSP_0132 metQ ABC D-methionine uptake transporter, substrate-binding protein (NCBI) 5, 263
RSP_0448 RSP_0448 EF-Tu; elongation factor Tu (NCBI) 209, 271
RSP_0490 RSP_0490 carbohydrate kinase (NCBI) 271, 363
RSP_0623 RSP_0623 hypothetical protein (NCBI) 65, 263
RSP_0624 RSP_0624 hypothetical protein (NCBI) 65, 263
RSP_0625 RSP_0625 Putative Maf-like protein (NCBI) 65, 263
RSP_0705 RSP_0705 Cytochrome cy (NCBI) 58, 271
RSP_0706 pheA Prephenate dehydratase (NCBI) 263, 271
RSP_0901 RSP_0901 N-6 Adenine-specific DNA methylase (NCBI) 142, 271
RSP_0902 RSP_0902 Hydrolase, haloacid dehalogenase-like hydrolase (NCBI) 142, 271
RSP_0970 RSP_0970 Putative citrate lyase beta chain (NCBI) 208, 263
RSP_1050 RSP_1050 Acetyltransferase (GNAT) family (NCBI) 5, 271
RSP_1051 RSP_1051 hypothetical protein (NCBI) 5, 271
RSP_1052 RSP_1052 possible Acetyltransferase (NCBI) 268, 271
RSP_1110 RSP_1110 hypothetical protein (NCBI) 209, 271
RSP_1132 RSP_1132 hypothetical protein (NCBI) 263, 271
RSP_1146 gltB Glutamine-pyruvate aminotransferase (NCBI) 231, 271
RSP_1287 RSP_1287 ABC branched chain amino acid family transporter, ATPase subunit (NCBI) 215, 263
RSP_1288 RSP_1288 ABC branched chain amino acid family transporter, ATPase subunit (NCBI) 263, 383
RSP_1289 RSP_1289 ABC branched chain amino acid family transporter, inner membrane subunit (NCBI) 130, 263
RSP_1290 RSP_1290 ABC branched chain amino acid family transporter, inner membrane subunit (NCBI) 263, 383
RSP_1291 RSP_1291 ABC branched chain amino acid family transporter, periplasmic substrate binding protein (NCBI) 263, 337
RSP_1474 nspC putative carboxynorspermidine decarboxylase protein (NCBI) 271, 323
RSP_1475 RSP_1475 saccharopine dehydrogenase family (NCBI) 271, 311
RSP_1575 sopT sulfate adenylyltransferase (NCBI) 109, 271
RSP_1675 rnc Ribonuclease III (NCBI) 263, 383
RSP_1849 RSP_1849 Aspartate kinase (NCBI) 109, 271
RSP_1874 carA Carbamoyl-phosphate synthase, small chain (NCBI) 258, 263
RSP_2170 RSP_2170 Phosphate transporter, Pit family (NCBI) 263, 383
RSP_2303 RSP_2303 hypothetical protein (NCBI) 54, 271
RSP_2612 fabH 3-oxoacyl-(acyl-carrier-protein) synthase III (NCBI) 263, 383
RSP_2613 plsX Fatty acid/phospholipid biosynthesis enzyme (NCBI) 263, 374
RSP_2699 RSP_2699 Probable GTP-binding protein (NCBI) 166, 271
RSP_2739 RSP_2739 hypothetical protein (NCBI) 5, 271
RSP_2918 RSP_2918 Predicted ferripyochelin binding protein (NCBI) 258, 263
RSP_2919 RSP_2919 Probable Guanylate kinase (NCBI) 258, 263
RSP_2920 RSP_2920 hypothetical protein (NCBI) 258, 263
RSP_2927 RSP_2927 ABC branched-chain amino acid transporter family, inner membrane subunit (NCBI) 65, 263
RSP_2950 RSP_2950 Transcriptional regulator, LysR family (NCBI) 7, 263
RSP_2977 prfB Peptide chain release factor 2 (NCBI) 271, 311
RSP_3547 RSP_3547 Ribonucleotide reductase (NCBI) 271, 311
RSP_3548 RSP_3548 hypothetical protein (NCBI) 181, 271
RSP_3591 RSP_3591 cytidylate kinase (NCBI) 209, 271
RSP_3600 miaB MiaB tRNA modification protein (Radical SAM) (NCBI) 271, 311
RSP_3829 RSP_3829 tRNA/rRNA methyltransferase (SpoU) (NCBI) 263, 271
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_0706
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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