Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1163 nusA

N-utilization substance protein A (NCBI)

CircVis
Functional Annotations (7)
Function System
Transcription elongation factor cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
RNA binding go/ molecular_function
protein binding go/ molecular_function
regulation of transcription termination, DNA-dependent go/ biological_process
NusA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1163
(Mouseover regulator name to see its description)

RSP_1163 is regulated by 18 influences and regulates 25 modules.
Regulators for RSP_1163 nusA (18)
Regulator Module Operator
RSP_0443 104 tf
RSP_0927 104 tf
RSP_1163 104 tf
RSP_1669 104 tf
RSP_1704 104 tf
RSP_1712 104 tf
RSP_1739 104 tf
RSP_2591 104 tf
RSP_3606 104 tf
RSP_0386 169 tf
RSP_0698 169 tf
RSP_1163 169 tf
RSP_1669 169 tf
RSP_1704 169 tf
RSP_1739 169 tf
RSP_2236 169 tf
RSP_2591 169 tf
RSP_3606 169 tf

Warning: RSP_1163 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
7928 1.20e+02 C.CcAaaacgaAag
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7929 1.40e+03 AaCCttGaAc.gcG
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8058 5.00e-01 AAaacgaAagaacg
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8059 6.60e+03 TCaCagtCGAA
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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_1163

RSP_1163 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Transcription elongation factor cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
RNA binding go/ molecular_function
protein binding go/ molecular_function
regulation of transcription termination, DNA-dependent go/ biological_process
NusA tigr/ tigrfam
Module neighborhood information for RSP_1163

RSP_1163 has total of 33 gene neighbors in modules 104, 169
Gene neighbors (33)
Gene Common Name Description Module membership
RSP_0140 RSP_0140 30S ribosomal protein S18 (NCBI) 169, 312
RSP_0141 RSP_0141 50S ribosomal protein L9 (NCBI) 104, 169
RSP_0827 RSP_0827 Ribosomal protein L25 (NCBI) 104, 166
RSP_1043 rpmE ribosomal protein L31 (NCBI) 169, 310
RSP_1044 rplS 50s ribosomal protein L19 (NCBI) 169, 310
RSP_1111 rpsO Ribosomal protein S15 (NCBI) 169, 310
RSP_1162 RSP_1162 hypothetical protein (NCBI) 104, 169
RSP_1163 nusA N-utilization substance protein A (NCBI) 104, 169
RSP_1164 RSP_1164 predicted nucleic-acid-binding protein (NCBI) 104, 212
RSP_1165 InfB Translation Initiation factor 2 (NCBI) 104, 169
RSP_1699 rpoB DNA-directed RNA polymerase, beta subunit (NCBI) 104, 169
RSP_1700 rplL 50S Ribosomal protein L7/L12 (NCBI) 104, 310
RSP_1701 rplJ Ribosomal protein L10 (NCBI) 169, 310
RSP_1702 rplA Ribosomal protein L1 (NCBI) 104, 169
RSP_1703 rplK Ribosomal protein L11 (NCBI) 104, 169
RSP_1704 RSP_1704 Probable transcription antitermination protein NusG (NCBI) 104, 310
RSP_1707 tufA Elongation factor Tu (EF-Tu) (NCBI) 169, 310
RSP_1712 rpoC RNA polymerase I subunit A, (NCBI) 104, 383
RSP_1723 rplP Ribosomal protein L16 (NCBI) 104, 224
RSP_1732 rpsE Ribosomal protein S5 (NCBI) 104, 272
RSP_1733 rpmD Ribosomal protein L30 (NCBI) 104, 224
RSP_1734 rplO 50S ribosomal protein L15 (NCBI) 104, 224
RSP_1737 rpsM Ribosomal protein S13 (NCBI) 151, 169
RSP_1738 rpsK Ribosomal protein S11 (NCBI) 151, 169
RSP_1764 rplT Ribosomal protein L20 (NCBI) 169, 310
RSP_1765 rpmI Ribosomal protein L35 (NCBI) 169, 310
RSP_2283 rpsD Ribosomal protein S4 (NCBI) 169, 312
RSP_2310 groES Chaperonin Cpn10 (GroES) (NCBI) 104, 312
RSP_2311 groEL Chaperonin Cpn60 (GroEL) (NCBI) 104, 312
RSP_2860 rpsB Ribosomal protein S2 (NCBI) 104, 169
RSP_2861 TSF Translation elongation factor Ts (NCBI) 104, 169
RSP_3819 rplU Ribosomal protein L21 (NCBI) 169, 312
RSP_3820 rpmA Ribosomal protein L27 (NCBI) 169, 309
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_1163
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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