Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2355

HNH nuclease / Probable phage PHI-105 holin-like protein (NCBI)

CircVis
Functional Annotations (2)
Function System
nucleic acid binding go/ molecular_function
endonuclease activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2355
(Mouseover regulator name to see its description)

RSP_2355 is regulated by 11 influences and regulates 0 modules.
Regulators for RSP_2355 (11)
Regulator Module Operator
RSP_0722 28 tf
RSP_1785 28 tf
RSP_1936 28 tf
RSP_2026 28 tf
RSP_2610 28 tf
RSP_2681 28 tf
RSP_3238 28 tf
RSP_3309 28 tf
RSP_1660 288 tf
RSP_3464 288 tf
RSP_3684 288 tf

Warning: RSP_2355 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
7776 2.20e+01 AaAcacC.aaaagctgcgTtTgA
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7777 6.00e+03 aGGagTtaAG
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8290 6.60e-02 caTgctcggaCat.aTCG.Ca
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8291 5.50e+00 AcatatCCcaTTgaatGcAaC
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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_2355

RSP_2355 is enriched for 2 functions in 2 categories.
Enrichment Table (2)
Function System
nucleic acid binding go/ molecular_function
endonuclease activity go/ molecular_function
Module neighborhood information for RSP_2355

RSP_2355 has total of 31 gene neighbors in modules 28, 288
Gene neighbors (31)
Gene Common Name Description Module membership
RSP_0180 RSP_0180 ABC nitrate/sulfonate/bicarbonate transporter, inner membrane subunit (NCBI) 23, 288
RSP_0207 RSP_0207 hypothetical protein (NCBI) 288, 303
RSP_0215 RSP_0215 hypothetical protein (NCBI) 242, 288
RSP_0340 RSP_0340 hypothetical protein (NCBI) 288, 296
RSP_0454 RSP_0454 multisensor hybrid histidine kinase (NCBI) 288, 313
RSP_0748 RSP_0748 N-6 Adenine-specific DNA methylase (NCBI) 68, 288
RSP_1114 RSP_1114 Hemolysin-type calcium-binding toxin (NCBI) 28, 236
RSP_1373 RSP_1373 Major facilitator superfamily (MFS) transporter (NCBI) 28, 44
RSP_1689 RSP_1689 hypothetical protein (NCBI) 28, 44
RSP_1784 RSP_1784 response regulator receiver domain protein (NCBI) 288, 296
RSP_1854 trkH3 potassium uptake transporter, transmembrane component, TrkH (NCBI) 67, 288
RSP_2025 RSP_2025 hypothetical protein (NCBI) 29, 288
RSP_2058 RSP_2058 hypothetical protein (NCBI) 31, 288
RSP_2259 RSP_2259 Transmembrane protein (NCBI) 288, 304
RSP_2262 RSP_2262 hypothetical protein (NCBI) 28, 125
RSP_2339 RSP_2339 hypothetical protein (NCBI) 28, 68
RSP_2355 RSP_2355 HNH nuclease / Probable phage PHI-105 holin-like protein (NCBI) 28, 288
RSP_2357 RSP_2357 hypothetical protein (NCBI) 288, 362
RSP_2559 RSP_2559 ABC transporter, fused ATPase and inner membrane subunits (NCBI) 247, 288
RSP_2958 RSP_2958 hypothetical protein (NCBI) 288, 308
RSP_3104 fdh Putative Glutathione-dependent formaldehyde dehydrogenase (NCBI) 288, 304
RSP_3106 RSP_3106 Cation efflux transporter, CDF family (NCBI) 105, 288
RSP_3123 RSP_3123 hypothetical protein (NCBI) 1, 288
RSP_3514 RSP_3514 transcriptional regulator, AraC family (NCBI) 288, 331
RSP_3515 RSP_3515 ABC polyamine/opine transporter, periplasmic binding protein (NCBI) 288, 331
RSP_3561 RSP_3561 hypothetical protein (NCBI) 288, 346
RSP_3659 RSP_3659 Predicted amidohydrolase (NCBI) 288, 304
RSP_3795 RSP_3795 hypothetical protein (NCBI) 247, 288
RSP_3798 RSP_3798 hypothetical protein (NCBI) 288, 380
RSP_3799 RSP_3799 hypothetical protein (NCBI) 288, 380
RSP_3813 parB ParB-like nuclease (NCBI) 189, 288
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_2355
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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