Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1915

Transcriptional regulator, LysR family (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1915
(Mouseover regulator name to see its description)

RSP_1915 is regulated by 16 influences and regulates 6 modules.
Regulators for RSP_1915 (16)
Regulator Module Operator
RSP_1014 83 tf
RSP_1077 83 tf
RSP_1790 83 tf
RSP_1915 83 tf
RSP_2351 83 tf
RSP_2965 83 tf
RSP_3001 83 tf
RSP_0068 101 tf
RSP_0090 101 tf
RSP_0728 101 tf
RSP_1191 101 tf
RSP_1660 101 tf
RSP_1741 101 tf
RSP_1871 101 tf
RSP_1915 101 tf
RSP_3528 101 tf

Warning: RSP_1915 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
7886 5.00e+04 TATGAA
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7887 9.30e+04 TgacGAGGt.CgtGAGgtagC
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7922 8.60e-11 cGgaAAAAaaGggCcgaagGGaAA
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7923 1.60e+00 gatCCttCCaccgAtaGGCcCTA
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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_1915

RSP_1915 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for RSP_1915

RSP_1915 has total of 34 gene neighbors in modules 83, 101
Gene neighbors (34)
Gene Common Name Description Module membership
RSP_0139 RSP_0139 Ribosomal protein S6 (NCBI) 83, 196
RSP_0144 RSP_0144 None 42, 101
RSP_0145 RSP_0145 None 13, 101
RSP_0176 RSP_0176 Dihydroxyacid dehydratase/phosphogluconate dehydratase (NCBI) 83, 242
RSP_0187 RSP_0187 Dihydroorotate dehydrogenase (NCBI) 83, 244
RSP_0492 hupU hydrogenase small subunit (NCBI) 83, 133
RSP_0616 RSP_0616 transcriptional regulator, AraC family (NCBI) 83, 88
RSP_0933 RSP_0933 hypothetical protein (NCBI) 69, 101
RSP_1184 RSP_1184 ribonuclease BN (NCBI) 83, 242
RSP_1533 RSP_1533 putative alginate O-acetyltransferase (NCBI) 101, 355
RSP_1534 RSP_1534 putative acyl carrier protein (NCBI) 101, 355
RSP_1535 RSP_1535 hypothetical protein (NCBI) 101, 355
RSP_1536 RSP_1536 conserved hypothetical protein that may be involved in lipid metabolism (NCBI) 56, 101
RSP_1537 RSP_1537 hypothetical protein (NCBI) 23, 101
RSP_1578 RSP_1578 conserved hypothetical protein TIGR00726 (NCBI) 101, 339
RSP_1579 RSP_1579 hypothetical protein (NCBI) 101, 339
RSP_1581 RSP_1581 hypothetical protein (NCBI) 101, 339
RSP_1650 RSP_1650 hypothetical protein (NCBI) 83, 313
RSP_1655 RSP_1655 hypothetical protein (NCBI) 61, 83
RSP_1898 RSP_1898 putative 5-formyltetrahydrofolate cyclo-ligase (NCBI) 63, 101
RSP_1915 RSP_1915 Transcriptional regulator, LysR family (NCBI) 83, 101
RSP_2352 RSP_2352 putative terminase large subunit / phage terminase (NCBI) 74, 83
RSP_2353 RSP_2353 hypothetical protein (NCBI) 74, 83
RSP_2354 RSP_2354 hypothetical protein (NCBI) 23, 83
RSP_2381 RSP_2381 putative 3-methyladenine DNA glycosylase (NCBI) 29, 101
RSP_2745 RSP_2745 hypothetical protein (NCBI) 22, 83
RSP_3017 RSP_3017 nitrilotriacetate monooxygenase (NCBI) 38, 83
RSP_3026 RSP_3026 Transcriptional regulator, MocR family (NCBI) 83, 168
RSP_3086 RSP_3086 periplasmic sensor signal transduction histidine kinase (NCBI) 83, 176
RSP_3105 RSP_3105 PAS sensor protein (NCBI) 83, 340
RSP_3130 RSP_3130 Putative serine protease (NCBI) 83, 244
RSP_3388 RSP_3388 putative Isocitrate/isopropylmalate dehydrogenase / tartrate dehydrogenase ttuC (NCBI) 83, 220
RSP_3528 RSP_3528 transcriptional regulator, TetR family (NCBI) 101, 177
RSP_3824 proA Gamma-glutamyl phosphate reductase GPR (NCBI) 30, 101
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_1915
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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