Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0505 hypA

Hydrogenase expression/synthesis, HypA family (NCBI)

CircVis
Functional Annotations (4)
Function System
Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) cog/ cog
protein modification process go/ biological_process
nickel ion binding go/ molecular_function
hypA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0505
(Mouseover regulator name to see its description)

RSP_0505 is regulated by 16 influences and regulates 0 modules.
Regulators for RSP_0505 hypA (16)
Regulator Module Operator
RSP_0489 199 tf
RSP_0507 199 tf
RSP_0999 199 tf
RSP_3165 199 tf
RSP_0071 245 tf
RSP_0489 245 tf
RSP_0507 245 tf
RSP_1163 245 tf
RSP_1164 245 tf
RSP_1590 245 tf
RSP_1776 245 tf
RSP_2130 245 tf
RSP_2200 245 tf
RSP_3165 245 tf
RSP_3324 245 tf
RSP_3620 245 tf

Warning: RSP_0505 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
8118 2.60e-03 TCgagCcAcAAtTcaAAAaaATAT
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8119 8.70e-02 atcaa.atatGaaaacgcct.ATc
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8208 1.80e+01 TTGTGAGGcAgAatCA
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8209 2.80e+02 tTtg..aatgg.tgcCaccctT.t
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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_0505

RSP_0505 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) cog/ cog
protein modification process go/ biological_process
nickel ion binding go/ molecular_function
hypA tigr/ tigrfam
Module neighborhood information for RSP_0505

RSP_0505 has total of 30 gene neighbors in modules 199, 245
Gene neighbors (30)
Gene Common Name Description Module membership
RSP_0030 RSP_0030 PAS sensor diguanylatecyclase/phosphodiesterase (NCBI) 60, 245
RSP_0041 RSP_0041 hypothetical protein (NCBI) 60, 245
RSP_0499 hupD HycI, hydrogenase maturation protease (NCBI) 199, 245
RSP_0500 RSP_0500 putative HupF/HypC hydrogenase protein (NCBI) 199, 245
RSP_0501 hupG HupG hydrogenase expression/formation protein (NCBI) 199, 245
RSP_0502 hupH HupH hydrogenase expression/formation protein (NCBI) 199, 245
RSP_0503 hupJ HupJ, contains rubredoxin domain (NCBI) 199, 245
RSP_0504 hupK HupK (NCBI) 199, 245
RSP_0505 hypA Hydrogenase expression/synthesis, HypA family (NCBI) 199, 245
RSP_0506 hypB NI2+-binding GTPase protein HypB (NCBI) 199, 245
RSP_0507 RSP_0507 HupR response regulator (NCBI) 199, 245
RSP_0508 hypC Hydrogenase expression/formation protein HypC (NCBI) 199, 245
RSP_0509 hypD hydrogenase isoenzymes formation protein HypD (NCBI) 199, 245
RSP_0510 hypE hydrogenase expression/formation protein HypE (NCBI) 199, 245
RSP_0513 RSP_0513 hypothetical protein (NCBI) 60, 245
RSP_0860 RSP_0860 hypothetical protein (NCBI) 245, 380
RSP_0861 RSP_0861 putative transmembrane hypothetical protein (NCBI) 60, 245
RSP_1144 Gst Glutathione S-transferase (NCBI) 67, 245
RSP_1627 RSP_1627 Putative N-6 adenine-specific DNA methylase (NCBI) 245, 379
RSP_1901 RSP_1901 Hypothetical protein with TPR repeat (NCBI) 91, 245
RSP_3165 RSP_3165 transcriptional regulator, GntR family (NCBI) 199, 337
RSP_3166 RSP_3166 ABC transporter, inner membrane subunit (NCBI) 199, 337
RSP_3167 RSP_3167 ABC transporter, ATPase subunit (NCBI) 199, 337
RSP_3168 RSP_3168 ABC transporter, periplasmic binding protein (NCBI) 199, 337
RSP_3169 RSP_3169 FAA-hydrolase-family protein (NCBI) 199, 337
RSP_3253 RSP_3253 Predicted acetamidase / formamidase (NCBI) 157, 245
RSP_3255 RSP_3255 ABC peptide transporter, periplasmic binding protein (NCBI) 157, 245
RSP_3769 RSP_3769 Adenine-specific DNA methyltransferase (NCBI) 245, 379
RSP_6014 RSP_6014 hypothetical protein (NCBI) 199, 257
RSP_6091 RSP_6091 hypothetical protein (NCBI) 199, 290
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_0505
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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