Organism : Geobacter sulfurreducens | Module List :
GSU3395 putA

proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase (NCBI)

CircVis
Functional Annotations (11)
Function System
Delta 1-pyrroline-5-carboxylate dehydrogenase cog/ cog
1-pyrroline-5-carboxylate dehydrogenase activity go/ molecular_function
proline dehydrogenase activity go/ molecular_function
glutamate biosynthetic process go/ biological_process
proline biosynthetic process go/ biological_process
proline catabolic process go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
D1pyr5carbox2 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3395
(Mouseover regulator name to see its description)

GSU3395 is regulated by 19 influences and regulates 0 modules.
Regulators for GSU3395 putA (19)
Regulator Module Operator
GSU0473 178 tf
GSU1410 178 tf
GSU1522 178 tf
GSU1626 178 tf
GSU1727 178 tf
GSU2926 178 tf
GSU3217 178 tf
GSU3229 178 tf
GSU0266 294 tf
GSU1522 294 tf
GSU1626 294 tf
GSU1727 294 tf
GSU1989 294 tf
GSU2262 294 tf
GSU2524 294 tf
GSU2581 294 tf
GSU3217 294 tf
GSU3363 294 tf
GSU3387 294 tf

Warning: GSU3395 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
2516 3.20e+01 GTATcTTTaCtAAGtAaccgATA
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2517 5.60e+03 tgCaa.accG.t.AtTGAcA
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2746 1.40e+03 ttTatttAtgaAtA.CATAa
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2747 8.00e+03 CCacTGctAgctTcctg.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 GSU3395

GSU3395 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Delta 1-pyrroline-5-carboxylate dehydrogenase cog/ cog
1-pyrroline-5-carboxylate dehydrogenase activity go/ molecular_function
proline dehydrogenase activity go/ molecular_function
glutamate biosynthetic process go/ biological_process
proline biosynthetic process go/ biological_process
proline catabolic process go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
D1pyr5carbox2 tigr/ tigrfam
Module neighborhood information for GSU3395

GSU3395 has total of 38 gene neighbors in modules 178, 294
Gene neighbors (38)
Gene Common Name Description Module membership
GSU0035 GSU0035 2',5' RNA ligase, putative (NCBI) 229, 294
GSU0188 GSU0188 conserved domain protein (VIMSS) 294, 339
GSU0202 GSU0202 conserved hypothetical protein (NCBI) 178, 339
GSU0245 GSU0245 glycosyl transferase, group 2 family protein (VIMSS) 119, 294
GSU0260 GSU0260 universal stress protein family (VIMSS) 14, 178
GSU0261 GSU0261 sodium/hydrogen exchanger family protein (VIMSS) 32, 178
GSU0266 GSU0266 transcriptional regulator, LysR family (VIMSS) 118, 294
GSU0450 GSU0450 conserved hypothetical protein (VIMSS) 178, 259
GSU0480 GSU0480 NifU-like domain protein (NCBI) 130, 178
GSU0710 GSU0710 hypothetical protein (VIMSS) 178, 288
GSU0728 GSU0728 conserved hypothetical protein (VIMSS) 178, 261
GSU0745 GSU0745 NAD-dependent dehydrogenase subunit (NCBI) 178, 238
GSU0840 GSU0840 hypothetical protein (VIMSS) 282, 294
GSU0884 GSU0884 radical SAM domain protein (NCBI) 217, 294
GSU0908 GSU0908 moaD family protein (NCBI) 13, 294
GSU0917 GSU0917 conserved hypothetical protein (VIMSS) 45, 294
GSU0971 prfA peptidyl-tRNA hydrolase domain protein (NCBI) 153, 178
GSU0974 GSU0974 hypothetical protein (VIMSS) 178, 250
GSU1090 GSU1090 signal transduction protein-related protein (VIMSS) 200, 294
GSU1147 GSU1147 conserved hypothetical protein (NCBI) 109, 294
GSU1376 GSU1376 hypothetical protein (VIMSS) 178, 218
GSU1723 GSU1723 mechanosensitive ion channel family protein (NCBI) 104, 294
GSU2098 cooS carbon monoxide dehydrogenase subunit (NCBI) 1, 178
GSU2144 GSU2144 sensor histidine kinase (VIMSS) 121, 294
GSU2145 vicR DNA-binding response regulator (NCBI) 294, 319
GSU2320 GSU2320 hypothetical protein (VIMSS) 92, 294
GSU2487 arcC carbamate kinase (NCBI) 178, 220
GSU2494 GSU2494 cytochrome c family protein (VIMSS) 46, 178
GSU2914 GSU2914 NHL repeat protein (NCBI) 178, 259
GSU2948 GSU2948 membrane protein, putative (NCBI) 103, 178
GSU3015 GSU3015 flagellin FlaG, putative (VIMSS) 217, 294
GSU3017 GSU3017 conserved domain protein (VIMSS) 178, 244
GSU3056 flhA flagellar biosynthetic protein FlhA (NCBI) 294, 312
GSU3103 hemK modification methylase, HemK family (NCBI) 118, 294
GSU3189 GSU3189 hypothetical protein (VIMSS) 178, 252
GSU3395 putA proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase (NCBI) 178, 294
GSU3396 GSU3396 transcriptional regulator, GntR family (VIMSS) 178, 295
GSU3460 GSU3460 glycosyl transferase, group 2 family protein (VIMSS) 118, 294
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 GSU3395
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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