Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1002 pyrB

Aspartate/ornithine carbamoyltransferase (NCBI)

CircVis
Functional Annotations (9)
Function System
Aspartate carbamoyltransferase, catalytic chain cog/ cog
aspartate carbamoyltransferase activity go/ molecular_function
'de novo' pyrimidine base biosynthetic process go/ biological_process
cellular amino acid metabolic process go/ biological_process
amino acid binding go/ molecular_function
Pyrimidine metabolism kegg/ kegg pathway
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
asp_carb_tr tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1002
(Mouseover regulator name to see its description)

RSP_1002 is regulated by 28 influences and regulates 0 modules.
Regulators for RSP_1002 pyrB (28)
Regulator Module Operator
RSP_0014 224 tf
RSP_1014 224 tf
RSP_1231 224 tf
RSP_1435 224 tf
RSP_1704 224 tf
RSP_1739 224 tf
RSP_2026 224 tf
RSP_2236 224 tf
RSP_2494 224 tf
RSP_2533 224 tf
RSP_2591 224 tf
RSP_2730 224 tf
RSP_2882 224 tf
RSP_2965 224 tf
RSP_3052 224 tf
RSP_3095 224 tf
RSP_3606 224 tf
RSP_0327 25 tf
RSP_0698 25 tf
RSP_0728 25 tf
RSP_0755 25 tf
RSP_0927 25 tf
RSP_1231 25 tf
RSP_2610 25 tf
RSP_2867 25 tf
RSP_3202 25 tf
RSP_3203 25 tf
RSP_3464 25 tf

Warning: RSP_1002 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
7770 7.30e+02 aAcGGtcAAgaacCa
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7771 4.50e+01 AcTtaaGgcGCtTcGCagaagcAt
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8166 2.00e+01 tTC.gGcGcTT
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8167 1.10e+02 gGAAgccAagaGgAt
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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_1002

RSP_1002 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Aspartate carbamoyltransferase, catalytic chain cog/ cog
aspartate carbamoyltransferase activity go/ molecular_function
'de novo' pyrimidine base biosynthetic process go/ biological_process
cellular amino acid metabolic process go/ biological_process
amino acid binding go/ molecular_function
Pyrimidine metabolism kegg/ kegg pathway
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
asp_carb_tr tigr/ tigrfam
Module neighborhood information for RSP_1002

RSP_1002 has total of 49 gene neighbors in modules 25, 224
Gene neighbors (49)
Gene Common Name Description Module membership
RSP_0021 rpsI Probable ribosomal protein S9 (NCBI) 151, 224
RSP_0147 glnA Glutamine synthetase class-I (NCBI) 25, 93
RSP_0250 RSP_0250 hypothetical protein (NCBI) 25, 278
RSP_0550 RSP_0550 putative D-alanyl-D-alanine carboxypeptidase (NCBI) 25, 52
RSP_0745 RSP_0745 acetyl-CoA acetyltransferase (NCBI) 25, 195
RSP_0747 RSP_0747 Short-chain dehydrogenase/reductase (NCBI) 25, 195
RSP_0915 RSP_0915 hypothetical protein (NCBI) 25, 278
RSP_0943 yhxA probable adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI) 25, 175
RSP_0968 mdh malate dehydrogenase (RefSeq) 25, 166
RSP_1002 pyrB Aspartate/ornithine carbamoyltransferase (NCBI) 25, 224
RSP_1003 pyrC Dihydroorotase and related cyclic amidohydrolases (NCBI) 224, 258
RSP_1112 Pnp polyribonucleotide nucleotidyltransferase (NCBI) 224, 310
RSP_1131 dapD 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI) 25, 192
RSP_1342 dnaA chromosomal replication initiator protein, DnaA (NCBI) 25, 381
RSP_1343 RSP_1343 DNA polymerase III, beta chain (NCBI) 25, 372
RSP_1345 RSP_1345 hypothetical protein (NCBI) 25, 262
RSP_1593 RSP_1593 NAD dependent malic enzyme (NCBI) 15, 25
RSP_1595 RSP_1595 Thymidine phosphorylase (NCBI) 15, 25
RSP_1598 RSP_1598 putative uracil phosphoribosyltransferase (NCBI) 15, 25
RSP_1613 RSP_1613 TRAP-T family transporter, DctP subunit (NCBI) 25, 291
RSP_1614 RSP_1614 TRAP-T family transporter with fused DctQ/DctM subunits (NCBI) 25, 112
RSP_1615 RSP_1615 hypothetical protein (NCBI) 25, 112
RSP_1674 RSP_1674 type 1 signal peptidase (NCBI) 224, 360
RSP_1676 era GTP-binding protein, Era-like (NCBI) 65, 224
RSP_1696 RSP_1696 DNA topoisomerase IV, A subunit (NCBI) 160, 224
RSP_1718 rplW 50S ribosomal protein L23 (NCBI) 224, 312
RSP_1723 rplP Ribosomal protein L16 (NCBI) 104, 224
RSP_1733 rpmD Ribosomal protein L30 (NCBI) 104, 224
RSP_1734 rplO 50S ribosomal protein L15 (NCBI) 104, 224
RSP_1735 secY Preprotein translocase SecY subunit (NCBI) 203, 224
RSP_1736 adk Adenylate kinase (NCBI) 47, 224
RSP_1797 YajC Putative preprotein translocase subunit YajC (NCBI) 224, 310
RSP_1798 SecD Protein-export membrane protein secD (NCBI) 224, 369
RSP_1799 secF protein-export membrane protein SecF (NCBI) 209, 224
RSP_1913 RSP_1913 3-oxoadipate CoA-transferase, beta subunit (NCBI) 25, 363
RSP_1914 RSP_1914 3-ketoacid CoA transferase alpha subunit (NCBI) 25, 363
RSP_1986 gatB Glutamyl-tRNA amidotransferase subunit B (NCBI) 25, 309
RSP_2131 rne Ribonuclease E (NCBI) 25, 223
RSP_2169 suhB Inositol monophosphatase family protein (NCBI) 182, 224
RSP_2465 RSP_2465 hypothetical protein (NCBI) 25, 203
RSP_2491 eno Enolase (NCBI) 224, 369
RSP_2614 rpmF possible 50S ribosomal protein L32 (NCBI) 75, 224
RSP_2622 ligA DNA ligase (NCBI) 25, 98
RSP_2778 RSP_2778 hypothetical protein (NCBI) 224, 268
RSP_2781 RSP_2781 peroxiredoxin/glutaredoxin family protein (NCBI) 25, 184
RSP_2868 RSP_2868 Putative inosine-5'-monophosphate dehydrogenase (NCBI) 224, 258
RSP_4047 pdhAa Pyruvate dehydrogenase E1 component, alpha subunit (NCBI) 25, 195
RSP_4049 pdhAb Pyruvate dehydrogenase E1 component, beta subunit (NCBI) 25, 291
RSP_4050 pdhB Dihydrolipoamide acetyltransferase component (E2) of pyruvate dehydrogenase complex (NCBI) 25, 291
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_1002
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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