Organism : Geobacter sulfurreducens | Module List :
GSU1542

transcriptional regulator, Cro/CI family (VIMSS)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
dnstrm_HI1420 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1542
(Mouseover regulator name to see its description)

GSU1542 is regulated by 15 influences and regulates 5 modules.
Regulators for GSU1542 (15)
Regulator Module Operator
GSU0473 180 tf
GSU1382 180 tf
GSU1569 180 tf
GSU2915 180 tf
GSU2987 180 tf
GSU3217 180 tf
GSU3387 180 tf
GSU3457 180 tf
GSU0013 235 tf
GSU0041 235 tf
GSU0280 235 tf
GSU1569 235 tf
GSU2262 235 tf
GSU2817 235 tf
GSU2987 235 tf

Warning: GSU1542 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
2520 5.80e+03 GAAaAAtA
Loader icon
2521 2.60e+04 AaTTtActgaA
Loader icon
2630 9.00e+03 ATAtTcTTAt
Loader icon
2631 3.40e+04 AATTAcCAtGATcAAAaTaAT
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 GSU1542

GSU1542 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
dnstrm_HI1420 tigr/ tigrfam
Module neighborhood information for GSU1542

GSU1542 has total of 44 gene neighbors in modules 180, 235
Gene neighbors (44)
Gene Common Name Description Module membership
GSU0105 GSU0105 cytochrome c family protein, putative (NCBI) 180, 181
GSU0282 GSU0282 hypothetical protein (VIMSS) 36, 180
GSU0401 GSU0401 methyl-accepting chemotaxis protein, putative (VIMSS) 216, 235
GSU0402 GSU0402 hemerythrin family protein (NCBI) 6, 235
GSU0403 cheY-1 chemotaxis protein CheY (NCBI) 216, 235
GSU0437 ubiD 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (NCBI) 99, 235
GSU0438 GSU0438 lipoprotein, putative (VIMSS) 54, 235
GSU0475 GSU0475 sensory box histidine kinase (VIMSS) 235, 317
GSU0477 GSU0477 hydrolase, haloacid dehalogenase-like family (NCBI) 235, 251
GSU0478 GSU0478 conserved hypothetical protein (VIMSS) 85, 235
GSU0479 aspA aspartate ammonia-lyase (NCBI) 85, 235
GSU0481 GSU0481 hypothetical protein (VIMSS) 85, 235
GSU0482 GSU0482 cardiolipin synthetase, putative (VIMSS) 166, 235
GSU0493 ndh NADH respiratory dehydrogenase (Regina ONeil) 133, 235
GSU0763 GSU0763 helicase, putative (NCBI) 130, 180
GSU0831 GSU0831 nitrogen regulatory protein P-II, putative (VIMSS) 27, 180
GSU0833 GSU0833 hypothetical protein (VIMSS) 180, 278
GSU0893 GSU0893 thioredoxin peroxidase (NCBI) 73, 235
GSU1214 GSU1214 tetracenomycin polyketide synthesis 8-o-methyltransferase, putative (NCBI) 148, 180
GSU1302 GSU1302 sensor histidine kinase/response regulator (VIMSS) 79, 180
GSU1542 GSU1542 transcriptional regulator, Cro/CI family (VIMSS) 180, 235
GSU1581 GSU1581 polyA polymerase family protein (NCBI) 130, 180
GSU1608 GSU1608 hypothetical protein (VIMSS) 193, 235
GSU1682 GSU1682 lipoprotein, putative (VIMSS) 42, 235
GSU1683 GSU1683 conserved hypothetical protein (VIMSS) 4, 235
GSU2374 GSU2374 hypothetical protein (VIMSS) 63, 180
GSU2512 GSU2512 hypothetical protein (VIMSS) 21, 180
GSU2532 GSU2532 conserved hypothetical protein (VIMSS) 180, 283
GSU2544 GSU2544 conserved hypothetical protein TIGR00044 (VIMSS) 235, 314
GSU2658 GSU2658 lipoprotein, putative (VIMSS) 180, 337
GSU2679 GSU2679 conserved hypothetical protein (VIMSS) 155, 180
GSU2774 GSU2774 hypothetical protein (VIMSS) 180, 232
GSU2795 GSU2795 iron-sulfur cluster-binding protein (VIMSS) 235, 251
GSU2796 etfA electron transfer flavoprotein, alpha subunit (NCBI) 235, 251
GSU2797 etfB electron transfer flavoprotein, beta subunit (NCBI) 114, 235
GSU2827 GSU2827 conserved hypothetical protein (VIMSS) 133, 235
GSU2828 GSU2828 GGDEF domain protein (VIMSS) 235, 280
GSU2965 GSU2965 conserved hypothetical protein (NCBI) 150, 235
GSU3119 GSU3119 sensor histidine kinase (VIMSS) 180, 278
GSU3180 GSU3180 conserved hypothetical protein (VIMSS) 1, 180
GSU3361 GSU3361 transglutaminase domain protein (NCBI) 180, 181
GSU3369 selA L-seryl-tRNA selenium transferase (NCBI) 148, 235
GSU3426 GSU3426 hypothetical protein (VIMSS) 148, 180
GSU3461 GSU3461 thioesterase family protein (NCBI) 216, 235
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 GSU1542
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