Organism : Geobacter sulfurreducens | Module List :
GSU1491

type IV pilus biogenesis protein PilB (VIMSS)

CircVis
Functional Annotations (8)
Function System
Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB cog/ cog
ATP binding go/ molecular_function
intracellular go/ cellular_component
transport go/ biological_process
protein transporter activity go/ molecular_function
pilus assembly go/ biological_process
nucleoside-triphosphatase activity go/ molecular_function
type_IV_pilB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1491
(Mouseover regulator name to see its description)

GSU1491 is regulated by 20 influences and regulates 0 modules.
Regulators for GSU1491 (20)
Regulator Module Operator
GSU0013 75 tf
GSU0031 75 tf
GSU0280 75 tf
GSU0359 75 tf
GSU0366 75 tf
GSU0372 75 tf
GSU0625 75 tf
GSU1522 75 tf
GSU1727 75 tf
GSU2523 75 tf
GSU2831 75 tf
GSU3229 75 tf
GSU0280 51 tf
GSU0770 51 tf
GSU1293 51 tf
GSU1495 51 tf
GSU1831 51 tf
GSU2524 51 tf
GSU3387 51 tf
GSU3396 51 tf

Warning: GSU1491 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
2262 5.00e+03 TtTCctttgg.
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2263 3.10e+04 TcagTttaTTcaCgtaATact
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2310 1.40e+03 CTctgcttAagTatAtCgGttaAt
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2311 8.90e+03 aTaTtAAAAaA
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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 GSU1491

GSU1491 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB cog/ cog
ATP binding go/ molecular_function
intracellular go/ cellular_component
transport go/ biological_process
protein transporter activity go/ molecular_function
pilus assembly go/ biological_process
nucleoside-triphosphatase activity go/ molecular_function
type_IV_pilB tigr/ tigrfam
Module neighborhood information for GSU1491

GSU1491 has total of 39 gene neighbors in modules 51, 75
Gene neighbors (39)
Gene Common Name Description Module membership
GSU0462 GSU0462 peptidase, M48 family (NCBI) 51, 63
GSU0463 GSU0463 membrane protein, putative (VIMSS) 36, 51
GSU0656 ilvE branched-chain amino acid aminotransferase (NCBI) 75, 183
GSU0702 GSU0702 cytochrome c family protein (VIMSS) 51, 76
GSU0821 GSU0821 conserved hypothetical protein (VIMSS) 8, 75
GSU0877 GSU0877 response regulator (VIMSS) 51, 76
GSU1155 GSU1155 glutaredoxin family protein (VIMSS) 51, 293
GSU1202 rfbA mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase, truncation (NCBI) 51, 144
GSU1246 dgt deoxyguanosinetriphosphate triphosphohydrolase, putative (NCBI) 75, 154
GSU1262 GSU1262 membrane protein, putative (VIMSS) 75, 176
GSU1314 GSU1314 membrane protein, putative (VIMSS) 75, 136
GSU1450 nth endonuclease III, putative (NCBI) 75, 227
GSU1488 GSU1488 membrane protein, putative (VIMSS) 75, 222
GSU1489 GSU1489 membrane protein, putative (VIMSS) 75, 199
GSU1491 GSU1491 type IV pilus biogenesis protein PilB (VIMSS) 51, 75
GSU1492 pilT-4 twitching motility protein PilT (NCBI) 75, 208
GSU1493 GSU1493 type IV pilus biogenesis protein PilC (VIMSS) 75, 313
GSU1517 rpmI ribosomal protein L35 (NCBI) 75, 161
GSU1564 GSU1564 Glu/Leu/Phe/Val dehydrogenase family protein (NCBI) 51, 76
GSU1572 GSU1572 ribD domain protein (NCBI) 51, 79
GSU1643 pleD GGDEF/response regulator receiver domain protein (NCBI) 51, 293
GSU1679 GSU1679 hypothetical protein (VIMSS) 51, 249
GSU1715 GSU1715 hypothetical protein (VIMSS) 51, 181
GSU2131 GSU2131 hypothetical protein (VIMSS) 51, 66
GSU2194 guaA GMP synthase (NCBI) 51, 201
GSU2216 GSU2216 PBS lyase HEAT-like repeat protein (NCBI) 51, 293
GSU2224 GSU2224 response regulator (VIMSS) 51, 201
GSU2291 GSU2291 phospho-2-dehydro-3-deoxyheptonate aldolase (VIMSS) 75, 227
GSU2377 GSU2377 hypothetical protein (VIMSS) 51, 158
GSU2450 GSU2450 conserved hypothetical protein (VIMSS) 51, 59
GSU2453 GSU2453 membrane protein, putative (VIMSS) 51, 79
GSU2554 GSU2554 conserved hypothetical protein (VIMSS) 51, 231
GSU2588 lpdA-2 alpha keto acid dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI) 75, 153
GSU2773 GSU2773 conserved domain protein (VIMSS) 51, 179
GSU2995 cobI precorrin-2 C20-methyltransferase (NCBI) 51, 76
GSU3004 GSU3004 cobalt transport protein CbiM (RefSeq) 75, 89
GSU3171 GSU3171 conserved domain protein (NCBI) 51, 103
GSU3250 pcnB polyA polymerase (NCBI) 51, 73
GSU3309 GSU3309 conserved hypothetical protein (VIMSS) 51, 121
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 GSU1491
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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