Organism : Geobacter sulfurreducens | Module List :
GSU1410

conserved hypothetical protein (VIMSS)

CircVis
Functional Annotations (5)
Function System
Predicted DNA-binding proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1410
(Mouseover regulator name to see its description)

GSU1410 is regulated by 18 influences and regulates 24 modules.
Regulators for GSU1410 (18)
Regulator Module Operator
GSU0366 202 tf
GSU0682 202 tf
GSU1410 202 tf
GSU2571 202 tf
GSU2945 202 tf
GSU2987 202 tf
GSU3127 202 tf
GSU3292 202 tf
GSU0205 112 tf
GSU0473 112 tf
GSU0812 112 tf
GSU1115 112 tf
GSU1410 112 tf
GSU1617 112 tf
GSU1727 112 tf
GSU2581 112 tf
GSU3396 112 tf
GSU3457 112 tf

Warning: GSU1410 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
2384 5.80e+03 tCcggcgCcgcaa.gGggtaA
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2385 2.80e+04 ttcTtTTaTTg
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2564 5.80e-10 tcttTt.TTGaAaTa
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2565 2.30e+01 aCCGAttggGc.atc.ttGCCCaT
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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 GSU1410

GSU1410 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted DNA-binding proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
Module neighborhood information for GSU1410

GSU1410 has total of 48 gene neighbors in modules 112, 202
Gene neighbors (48)
Gene Common Name Description Module membership
GSU0154 GSU0154 mutT/nudix family protein (NCBI) 112, 289
GSU0178 GSU0178 conserved hypothetical protein (VIMSS) 157, 202
GSU0179 GSU0179 NADPH-dependent FMN reductase domain protein (NCBI) 202, 230
GSU0180 GSU0180 conserved hypothetical protein (VIMSS) 35, 202
GSU0205 GSU0205 transcriptional regulator, TetR family (VIMSS) 112, 289
GSU0483 GSU0483 exsB protein (VIMSS) 112, 289
GSU0793 GSU0793 hypothetical protein (VIMSS) 202, 289
GSU0794 GSU0794 pyridine nucleotide-disulfide oxidoreductase/rhodanese domain protein (NCBI) 114, 202
GSU0888 GSU0888 hypothetical protein (NCBI) 35, 202
GSU1005 nifR3 dihydrouridine synthase family protein (NCBI) 112, 333
GSU1080 GSU1080 hypothetical protein (VIMSS) 112, 206
GSU1081 GSU1081 conserved hypothetical protein (VIMSS) 202, 298
GSU1180 ftsH-1 cell division protein FtsH (NCBI) 112, 126
GSU1194 GSU1194 transporter, LysE family (VIMSS) 67, 112
GSU1221 GSU1221 ammonium transporter, putative (VIMSS) 64, 202
GSU1235 GSU1235 conserved hypothetical protein (VIMSS) 72, 202
GSU1236 GSU1236 conserved hypothetical protein (NCBI) 72, 202
GSU1239 gltB glutamate synthase-related protein (NCBI) 114, 202
GSU1258 nosL nosL protein (NCBI) 176, 202
GSU1408 GSU1408 ParA family protein (VIMSS) 202, 331
GSU1409 GSU1409 NifU-like domain protein (NCBI) 202, 331
GSU1410 GSU1410 conserved hypothetical protein (VIMSS) 112, 202
GSU1411 GSU1411 sodium/bile acid symporter family protein (VIMSS) 202, 331
GSU1412 GSU1412 hypothetical protein (VIMSS) 202, 331
GSU1738 GSU1738 indolepyruvate ferredoxin oxidoreductase, beta subunit (VIMSS) 112, 136
GSU1832 GSU1832 conserved hypothetical protein (NCBI) 112, 289
GSU2083 rfbA glucose-1-phosphate thymidylyltransferase (NCBI) 112, 333
GSU2213 GSU2213 GAF domain protein (VIMSS) 47, 112
GSU2364 rfbA mannose-6-phosphate isomerase (NCBI) 112, 156
GSU2565 GSU2565 sensor histidine kinase (VIMSS) 112, 156
GSU2567 GSU2567 sensor histidine kinase (VIMSS) 112, 144
GSU2722 GSU2722 NAD-reducing hydrogenase, putative (VIMSS) 112, 128
GSU2771 GSU2771 conserved hypothetical protein (VIMSS) 193, 202
GSU2807 GSU2807 conserved hypothetical protein (VIMSS) 35, 202
GSU2936 GSU2936 hypothetical protein (VIMSS) 202, 331
GSU2937 GSU2937 cytochrome c family protein (NCBI) 202, 331
GSU2938 GSU2938 hypothetical protein (VIMSS) 22, 202
GSU2939 GSU2939 outer membrane porin FmdC, putative (VIMSS) 22, 202
GSU2940 GSU2940 lipoprotein, putative (VIMSS) 202, 331
GSU2986 znuA periplasmic component of zinc ABC transporter (Dmitry Rodionov) 193, 202
GSU2987 Zur Zinc uptake transcriptional regulator (Fur family) (Dmitry Rodionov) 129, 202
GSU2990 cobD cobalamin biosynthesis protein CobD (NCBI) 112, 289
GSU3080 GSU3080 hypothetical protein (VIMSS) 112, 207
GSU3113 GSU3113 metallo-beta-lactamase family protein (VIMSS) 112, 128
GSU3291 GSU3291 V-type H(+)-translocating pyrophosphatase (VIMSS) 162, 202
GSU3292 GSU3292 transcriptional regulator, Fur family (VIMSS) 35, 202
GSU3383 gatC glutamyl-tRNA(Gln) amidotransferase, C subunit (NCBI) 112, 289
GSU3457 GSU3457 glycine cleavage system transcriptional repressor, putative (VIMSS) 112, 289
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 GSU1410
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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