Organism : Geobacter sulfurreducens | Module List :
GSU1379 fur

ferric uptake regulation protein (Dmitry Rodionov)

CircVis
Functional Annotations (3)
Function System
Fe2+/Zn2+ uptake regulation proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1379
(Mouseover regulator name to see its description)

GSU1379 is regulated by 17 influences and regulates 1 modules.
Regulators for GSU1379 fur (17)
Regulator Module Operator
GSU0187 81 tf
GSU0284 81 tf
GSU0300 81 tf
GSU0514 81 tf
GSU0625 81 tf
GSU0735 81 tf
GSU1268 81 tf
GSU1831 81 tf
GSU3060 81 tf
GSU3087 81 tf
GSU0178 121 tf
GSU0266 121 tf
GSU1410 121 tf
GSU1831 121 tf
GSU1989 121 tf
GSU2524 121 tf
GSU3370 121 tf
Regulated by GSU1379 (1)
Module Residual Genes
230 0.38 19
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
2322 2.60e+03 cCCtcTTT
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2323 4.00e+03 AAATAt
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2402 6.70e+00 atGaacttaActttcagTT
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2403 8.40e+02 TaTCcCTtgtgttagaacaaaAAa
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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 GSU1379

GSU1379 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Fe2+/Zn2+ uptake regulation proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for GSU1379

GSU1379 has total of 39 gene neighbors in modules 81, 121
Gene neighbors (39)
Gene Common Name Description Module membership
GSU0065 GSU0065 cytidine/deoxycytidylate deaminase family protein (VIMSS) 81, 200
GSU0501 GSU0501 lipoprotein, putative (VIMSS) 114, 121
GSU0503 crcB crcB protein (NCBI) 77, 121
GSU0504 GSU0504 conserved hypothetical protein (VIMSS) 121, 284
GSU0508 GSU0508 conserved hypothetical protein TIGR00247 (NCBI) 7, 121
GSU0514 GSU0514 transcriptional regulator, IclR family (VIMSS) 81, 86
GSU0522 rhlB ATP-dependent RNA helicase RhlB (NCBI) 81, 133
GSU0617 GSU0617 NHL repeat domain protein (VIMSS) 121, 148
GSU0661 prsA ribose-phosphate pyrophosphokinase (NCBI) 35, 81
GSU0729 GSU0729 iron-sulfur cluster-binding protein (VIMSS) 121, 291
GSU0807 GSU0807 apo-citrate lyase phosphoribosyl-dephospho-CoA transferase, putative (NCBI) 81, 200
GSU0927 GSU0927 peptidase, M16 family (NCBI) 20, 121
GSU1133 GSU1133 hypothetical protein (VIMSS) 81, 276
GSU1134 GSU1134 conserved hypothetical protein (VIMSS) 81, 307
GSU1151 GSU1151 conserved hypothetical protein (VIMSS) 121, 277
GSU1293 GSU1293 DNA-binding response regulator, LuxR family (VIMSS) 76, 81
GSU1353 GSU1353 prevent-host-death family protein (NCBI) 81, 159
GSU1379 fur ferric uptake regulation protein (Dmitry Rodionov) 81, 121
GSU1381 GSU1381 hypothetical protein (VIMSS) 121, 324
GSU1490 aroE shikimate 5-dehydrogenase (NCBI) 83, 121
GSU1571 GSU1571 conserved domain protein (NCBI) 121, 153
GSU1631 GSU1631 metallo-beta-lactamase family protein (VIMSS) 81, 315
GSU1893 GSU1893 carbohydrate isomerase, KpsF/GutQ family (VIMSS) 81, 306
GSU1916 cdsA phosphatidate cytidylyltransferase (NCBI) 81, 277
GSU2032 GSU2032 type IV pilus biogenesis protein PilM (VIMSS) 76, 81
GSU2068 GSU2068 6-phosphofructokinase (VIMSS) 88, 121
GSU2089 mreB rod shape-determining protein MreB (NCBI) 81, 162
GSU2129 GSU2129 hypothetical protein (VIMSS) 121, 324
GSU2144 GSU2144 sensor histidine kinase (VIMSS) 121, 294
GSU2304 GSU2304 hypothetical protein (VIMSS) 81, 162
GSU2393 GSU2393 ISGsu5, transposase, truncation (VIMSS) 121, 189
GSU2607 tyrA prephenate dehydrogenase (NCBI) 81, 145
GSU2608 pheA chorismate mutase/prephenate dehydratase (NCBI) 76, 81
GSU2789 GSU2789 sensory box histidine kinase (VIMSS) 121, 269
GSU3116 GSU3116 1-acyl-sn-glycerol-3-phosphate acyltransferase, putative (NCBI) 81, 189
GSU3208 GSU3208 conserved hypothetical protein (NCBI) 88, 121
GSU3212 proB glutamate 5-kinase (NCBI) 121, 160
GSU3309 GSU3309 conserved hypothetical protein (VIMSS) 51, 121
GSU3364 GSU3364 hypothetical protein (VIMSS) 81, 189
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 GSU1379
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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