Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0496 hupL

hydrogenase protein large subunit (NCBI)

CircVis
Functional Annotations (7)
Function System
Ni,Fe-hydrogenase I large subunit cog/ cog
electron transport go/ biological_process
ferredoxin hydrogenase activity go/ molecular_function
nickel ion binding go/ molecular_function
hydrogenase (acceptor) activity go/ molecular_function
Nitrotoluene degradation kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0496
(Mouseover regulator name to see its description)

RSP_0496 is regulated by 25 influences and regulates 0 modules.
Regulators for RSP_0496 hupL (25)
Regulator Module Operator
RSP_0122 253 tf
RSP_1014 253 tf
RSP_1231 253 tf
RSP_1776 253 tf
RSP_1871 253 tf
RSP_2130 253 tf
RSP_2425 253 tf
RSP_2610 253 tf
RSP_3309 253 tf
RSP_3322 253 tf
RSP_3339 253 tf
RSP_3464 253 tf
RSP_0591 300 tf
RSP_0641 300 tf
RSP_1231 300 tf
RSP_1590 300 tf
RSP_1776 300 tf
RSP_1790 300 tf
RSP_1871 300 tf
RSP_2130 300 tf
RSP_2610 300 tf
RSP_2867 300 tf
RSP_3322 300 tf
RSP_3464 300 tf
RSP_3684 300 tf

Warning: RSP_0496 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
8224 1.60e+01 GaTcTCctTcgGcG
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8225 6.80e+02 catGgcGactT
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8314 4.20e+02 AaAAGAAA
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8315 5.30e+03 AtggtCaCGAT
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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_0496

RSP_0496 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Ni,Fe-hydrogenase I large subunit cog/ cog
electron transport go/ biological_process
ferredoxin hydrogenase activity go/ molecular_function
nickel ion binding go/ molecular_function
hydrogenase (acceptor) activity go/ molecular_function
Nitrotoluene degradation kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for RSP_0496

RSP_0496 has total of 50 gene neighbors in modules 253, 300
Gene neighbors (50)
Gene Common Name Description Module membership
RSP_0301 RSP_0301 ABC branched chain amino acid transporter, substrate binding protein (NCBI) 68, 300
RSP_0481 RSP_0481 possible 2-deoxy-D-gluconate 3-dehydrogenase (NCBI) 253, 301
RSP_0495 hupS hydrogenase protein small subunit (NCBI) 253, 300
RSP_0496 hupL hydrogenase protein large subunit (NCBI) 253, 300
RSP_0497 RSP_0497 HupE/UreJ accessory protein (NCBI) 253, 300
RSP_0498 hupC Ni, Fe hydrogenase I cytochrome b subunit (NCBI) 244, 300
RSP_0542 RSP_0542 hypothetical protein (NCBI) 244, 300
RSP_0545 RSP_0545 hypothetical protein (NCBI) 141, 300
RSP_0644 RSP_0644 ABC transporter, inner membrane subunit (NCBI) 253, 347
RSP_0645 RSP_0645 ABC transporter, ATPase subunit (NCBI) 253, 347
RSP_0646 RSP_0646 ABC transporter, substrate-binding protein (NCBI) 253, 347
RSP_0647 thiD phosphomethylpyrimidine kinase (NCBI) 253, 347
RSP_0648 thiE Thiamine-phosphate pyrophosphorylase (NCBI) 253, 347
RSP_0649 thiM Putative hydoxyethylthiazole kinase (NCBI) 253, 347
RSP_0961 MeaA similiar to methylmalonyl-CoA mutases (NCBI) 14, 253
RSP_1299 RSP_1299 putative binding domain (NCBI) 253, 303
RSP_1509 RSP_1509 Glycoprotease (M22) metalloprotease (NCBI) 292, 300
RSP_1639 RSP_1639 hypothetical protein (NCBI) 233, 253
RSP_1641 RSP_1641 hypothetical protein (NCBI) 233, 300
RSP_1643 RSP_1643 hypothetical protein (NCBI) 236, 300
RSP_1644 RSP_1644 hypothetical protein (NCBI) 233, 300
RSP_1661 RSP_1661 hypothetical protein (NCBI) 292, 300
RSP_1751 RSP_1751 putative 2Fe-2S ferredoxin protein (NCBI) 244, 300
RSP_1920 RSP_1920 Pyridoxal/pyridoxine/pyridoxamine kinase (NCBI) 99, 253
RSP_1921 RSP_1921 MOSC domain protein (NCBI) 99, 253
RSP_2063 RSP_2063 hypothetical protein (NCBI) 253, 303
RSP_2498 RSP_2498 None 74, 300
RSP_2620 RSP_2620 hypothetical protein (NCBI) 191, 300
RSP_3016 RSP_3016 Possible phenol degradation enzyme (NCBI) 137, 300
RSP_3019 RSP_3019 putative hydrolase (NCBI) 137, 300
RSP_3021 RSP_3021 putative catechol 2,3-dioxygenase (NCBI) 137, 300
RSP_3188 RSP_3188 ApbE family protein (NCBI) 244, 300
RSP_3191 fprA Flavodoxin (NCBI) 244, 300
RSP_3199 RSP_3199 hypothetical protein (NCBI) 244, 300
RSP_3242 RSP_3242 Putative trypsin-like serine protease (NCBI) 253, 331
RSP_3339 RSP_3339 transcriptional regulator, GntR family (NCBI) 38, 253
RSP_3355 RSP_3355 putative tape measure protein (NCBI) 38, 300
RSP_3391 RSP_3391 ABC Fe3+-siderophores transporter, inner membrane subunit (NCBI) 188, 253
RSP_3413 RSP_3413 ABC Fe+3-siderophore transporter, ATPase subunit (NCBI) 138, 253
RSP_3577 gvpG putative gas vesicle synthesis protein (NCBI) 253, 304
RSP_3578 gvpF2 putative gas vesicle synthesis protein (NCBI) 153, 253
RSP_3579 RSP_3579 Heat shock protein Hsp20 (NCBI) 196, 253
RSP_3580 gvpJ Gas vesicle protein GVPa (NCBI) 253, 282
RSP_3581 RSP_3581 hypothetical protein (NCBI) 196, 253
RSP_3582 gvpN ATPase (NCBI) 153, 253
RSP_3612 RSP_3612 hypothetical protein (NCBI) 153, 300
RSP_3630 RSP_3630 hypothetical protein (NCBI) 246, 253
RSP_3631 RSP_3631 hypothetical protein (NCBI) 73, 253
RSP_3690 RSP_3690 resiniferatoxin-binding, phosphotriesterase-related protein (NCBI) 31, 253
RSP_3796 RSP_3796 hypothetical protein (NCBI) 253, 282
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_0496
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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