Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0728

hypothetical protein (NCBI)

CircVis
Functional Annotations (4)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0728
(Mouseover regulator name to see its description)

RSP_0728 is regulated by 24 influences and regulates 23 modules.
Regulators for RSP_0728 (24)
Regulator Module Operator
RSP_0457 164 tf
RSP_0728 164 tf
RSP_1776 164 tf
RSP_1892 164 tf
RSP_2130 164 tf
RSP_2362 164 tf
RSP_2494 164 tf
RSP_3064 164 tf
RSP_3322 164 tf
RSP_3339 164 tf
RSP_3684 164 tf
RSP_0511 299 tf
RSP_0728 299 tf
RSP_0774 299 tf
RSP_1231 299 tf
RSP_1739 299 tf
RSP_1776 299 tf
RSP_1892 299 tf
RSP_2027 299 tf
RSP_2850 299 tf
RSP_2867 299 tf
RSP_2922 299 tf
RSP_3109 299 tf
RSP_3664 299 tf

Warning: RSP_0728 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
8048 1.50e+03 cTGATC
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8049 1.10e+04 AtGcccaGaAGcCC
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8312 2.70e+02 AaGAaaacgcAAA
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8313 4.30e+01 catctgCgGCTTtCg
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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_0728

RSP_0728 is enriched for 4 functions in 2 categories.
Enrichment Table (4)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for RSP_0728

RSP_0728 has total of 35 gene neighbors in modules 164, 299
Gene neighbors (35)
Gene Common Name Description Module membership
RSP_0358 gor probable glutathione reductase (NCBI) 234, 299
RSP_0403 RSP_0403 homoserine dehydrogenase (NCBI) 109, 299
RSP_0553 ruvB Holiday junction DNA helicase RuvB (NCBI) 299, 372
RSP_0727 RSP_0727 hypothetical protein (NCBI) 164, 299
RSP_0728 RSP_0728 hypothetical protein (NCBI) 164, 299
RSP_0743 RSP_0743 Putative translation factor (NCBI) 149, 299
RSP_0934 gpmI Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent (NCBI) 192, 299
RSP_1008 RSP_1008 4-hydroxybenzoate octaprenyltransferase (NCBI) 71, 164
RSP_1009 RSP_1009 possible outer membrane protein, OmpA family (NCBI) 71, 164
RSP_1011 RSP_1011 hypothetical protein (NCBI) 69, 164
RSP_1028 RSP_1028 DNA polymerase I (NCBI) 164, 212
RSP_1105 DapB Dihydrodipicolinate reductase (DHPR) (NCBI) 268, 299
RSP_1218 mutS DNA mismatch repair protein MutS (NCBI) 209, 299
RSP_1470 rnhB ribonuclease HII (NCBI) 84, 164
RSP_1514 ahcY Adenosylhomocysteinase (NCBI) 299, 360
RSP_1801 ccmA ABC heme exporter, ATPase subunt CcmA (NCBI) 149, 299
RSP_1802 ccmB ABC heme exporter, inner membrane subunit CcmB (NCBI) 196, 299
RSP_1803 ccmC ABC heme exporter, inner membrane subunit CcmC (NCBI) 149, 299
RSP_1804 ccmD Heme exporter protein D (NCBI) 149, 299
RSP_1805 ccmG Probable thiol-disulfide interchange protein (NCBI) 149, 299
RSP_1846 RSP_1846 hypothetical protein (NCBI) 133, 164
RSP_1869 RSP_1869 Putative oxidoreductase protein (NCBI) 63, 164
RSP_2095 RSP_2095 Putative MraZ protein (NCBI) 261, 299
RSP_2114 ftsZ1 Cell division protein, FtsZ, GTPase (NCBI) 261, 299
RSP_2124 RSP_2124 hypothetical protein (NCBI) 164, 298
RSP_2144 cfaS Cyclopropane-fatty-acyl-phospholipid synthase CfaS (NCBI) 299, 311
RSP_2146 trgB Tellurite resistance protein (NCBI) 158, 299
RSP_2159 RSP_2159 ABC transporter, ATPase subunit (NCBI) 59, 299
RSP_2333 nadE NH3 dependent NAD synthetase, NadE (NCBI) 72, 299
RSP_2455 RSP_2455 putative Colicin V production protein, dedE (NCBI) 109, 299
RSP_2744 RSP_2744 hypothetical protein (NCBI) 214, 299
RSP_2946 argC N-acetyl-gamma-glutamyl-phosphate reductase (NCBI) 299, 323
RSP_3722 RSP_3722 hypothetical protein (NCBI) 164, 335
RSP_4044 pgk Phosphoglycerate kinase (NCBI) 166, 299
RSP_4045 fbaB Fructose-bisphosphate aldolase class I (NCBI) 166, 299
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_0728
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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