Organism : Geobacter sulfurreducens | Module List :
GSU2237 rpoZ

DNA-directed RNA polymerase, omega subunit (NCBI)

CircVis
Functional Annotations (12)
Function System
DNA-directed RNA polymerase, subunit K/omega cog/ cog
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoZ tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2237
(Mouseover regulator name to see its description)

GSU2237 is regulated by 24 influences and regulates 19 modules.
Regulators for GSU2237 rpoZ (24)
Regulator Module Operator
GSU0372 169 tf
GSU0655 169 tf
GSU1129 169 tf
GSU1692 169 tf
GSU1989 169 tf
GSU2041 169 tf
GSU2237 169 tf
GSU2354 169 tf
GSU2524 169 tf
GSU2666 169 tf
GSU3087 169 tf
GSU0736 228 tf
GSU1115 228 tf
GSU1250 228 tf
GSU1382 228 tf
GSU1569 228 tf
GSU2237 228 tf
GSU2524 228 tf
GSU2831 228 tf
GSU2915 228 tf
GSU3217 228 tf
GSU3370 228 tf
GSU3421 228 tf
GSU3457 228 tf

Warning: GSU2237 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
2498 2.00e+02 acaaGcaAcTGa.aa
Loader icon
2499 2.40e+03 TtAtTtc.TAaAccc
Loader icon
2616 6.90e-01 TaTTtAtTTttcTttacgGGGTGA
Loader icon
2617 7.90e+01 AAaAcCtTT.C
Loader icon
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 GSU2237

GSU2237 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
DNA-directed RNA polymerase, subunit K/omega cog/ cog
DNA binding go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription, DNA-dependent go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoZ tigr/ tigrfam
Module neighborhood information for GSU2237

GSU2237 has total of 48 gene neighbors in modules 169, 228
Gene neighbors (48)
Gene Common Name Description Module membership
GSU0024 GSU0024 OmpA domain protein (VIMSS) 228, 258
GSU0088 GSU0088 heterodisulfide reductase subunit (VIMSS) 169, 214
GSU0111 atpA ATP synthase F1, alpha subunit (NCBI) 10, 169
GSU0197 GSU0197 oxidoreductase, short chain dehydrogenase/reductase family (VIMSS) 80, 169
GSU0212 GSU0212 ABC transporter, ATP-binding protein (VIMSS) 228, 309
GSU0298 GSU0298 sigma-54 dependent DNA-binding response regulator, interruption-C (VIMSS) 116, 169
GSU0455 GSU0455 rare lipoprotein A domain protein (VIMSS) 50, 228
GSU0505 GSU0505 rhodanese-like domain protein (VIMSS) 228, 238
GSU0648 rplS ribosomal protein L19 (NCBI) 228, 267
GSU0660 ispE 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (NCBI) 18, 228
GSU0826 GSU0826 hypothetical protein (VIMSS) 228, 238
GSU0869 GSU0869 LysM domain/NLP/P60 family protein (NCBI) 50, 228
GSU0871 GSU0871 radical SAM domain protein/B12 binding domain protein (NCBI) 50, 169
GSU1149 GSU1149 EAL domain protein (NCBI) 60, 228
GSU1176 GSU1176 fumarate reductase, cytochrome b subunit, putative (VIMSS) 101, 228
GSU1178 frdB fumarate reductase, iron-sulfur protein (NCBI) 225, 228
GSU1375 GSU1375 hypothetical protein (VIMSS) 169, 225
GSU1496 GSU1496 pilin domain protein (VIMSS) 117, 169
GSU1497 GSU1497 hypothetical protein (VIMSS) 117, 169
GSU1599 rpmF ribosomal protein L32 (NCBI) 62, 169
GSU1660 acnB aconitate hydratase 2 (NCBI) 101, 169
GSU1886 yfiA ribosomal subunit interface protein (NCBI) 169, 238
GSU1888 GSU1888 ABC transporter, ATP-binding protein (VIMSS) 50, 228
GSU1889 GSU1889 conserved hypothetical protein (VIMSS) 50, 228
GSU1890 GSU1890 hypothetical protein (VIMSS) 50, 228
GSU1902 leuD 3-isopropylmalate dehydratase, small subunit, putative (NCBI) 101, 169
GSU1911 ilvB acetolactate synthase, large subunit, biosynthetic type (NCBI) 228, 276
GSU2206 rpsT ribosomal protein S20 (NCBI) 228, 297
GSU2237 rpoZ DNA-directed RNA polymerase, omega subunit (NCBI) 169, 228
GSU2563 GSU2563 conserved hypothetical protein (VIMSS) 26, 228
GSU2621 spoIID stage II sporulation-related protein (NCBI) 50, 228
GSU2642 GSU2642 cytochrome c family protein (NCBI) 136, 169
GSU2645 GSU2645 cytochrome c family protein (NCBI) 169, 215
GSU2708 GSU2708 ferredoxin family protein (VIMSS) 101, 228
GSU2998 GSU2998 nitroimidazole resistance protein, putative (VIMSS) 89, 169
GSU3005 thiC-2 thiamine biosynthesis protein ThiC (NCBI) 101, 169
GSU3007 GSU3007 phosphoglycerate mutase family, putative (VIMSS) 101, 169
GSU3009 cobT nicotinate-nucleotide--dimethylbenzimidazolephosphoribosyltransferase (NCBI) 101, 169
GSU3117 ssb-2 single-strand binding protein (NCBI) 35, 228
GSU3136 ileS isoleucyl-tRNA synthetase (NCBI) 228, 238
GSU3243 GSU3243 hypothetical protein (VIMSS) 50, 228
GSU3278 GSU3278 hypothetical protein (VIMSS) 169, 276
GSU3340 groeL 60 kDa chaperonin (NCBI) 50, 228
GSU3401 GSU3401 branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein, putative (NCBI) 117, 169
GSU3402 GSU3402 hypothetical protein (VIMSS) 117, 169
GSU3403 GSU3403 hypothetical protein (VIMSS) 117, 169
GSU3406 GSU3406 amino acid ABC transporter, periplasmic amino acid-binding protein (NCBI) 117, 169
GSU3453 hemE uroporphyrinogen decarboxylase (NCBI) 50, 228
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 GSU2237
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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