Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3805

possible integrase (NCBI)

CircVis
Functional Annotations (4)
Function System
Site-specific recombinase XerC cog/ cog
DNA binding go/ molecular_function
DNA recombination go/ biological_process
DNA integration go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3805
(Mouseover regulator name to see its description)

RSP_3805 is regulated by 20 influences and regulates 0 modules.
Regulators for RSP_3805 (20)
Regulator Module Operator
RSP_0907 157 tf
RSP_1231 157 tf
RSP_1518 157 tf
RSP_3029 157 tf
RSP_3700 157 tf
RSP_0018 285 tf
RSP_0186 285 tf
RSP_0386 285 tf
RSP_1014 285 tf
RSP_1055 285 tf
RSP_1704 285 tf
RSP_1890 285 tf
RSP_1990 285 tf
RSP_2026 285 tf
RSP_2351 285 tf
RSP_3029 285 tf
RSP_3042 285 tf
RSP_3109 285 tf
RSP_3124 285 tf
RSP_3322 285 tf

Warning: RSP_3805 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
8034 1.80e-04 Ata.aTCAgtgCa.ataatCtcAA
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8035 1.00e-01 CATGGTTccGCaatCGaaAGa
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8284 9.40e-06 tgGtATcaacAtaA.AgGc
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8285 4.10e+00 gcgcATCcaGtcGgacaagCatAc
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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 RSP_3805

RSP_3805 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Site-specific recombinase XerC cog/ cog
DNA binding go/ molecular_function
DNA recombination go/ biological_process
DNA integration go/ biological_process
Module neighborhood information for RSP_3805

RSP_3805 has total of 60 gene neighbors in modules 157, 285
Gene neighbors (60)
Gene Common Name Description Module membership
RSP_0018 RSP_0018 Putative transcriptional regulator, gntR family (NCBI) 285, 326
RSP_0019 RSP_0019 hypothetical protein (NCBI) 48, 285
RSP_0204 RSP_0204 metallo-beta-lactamase family protein (NCBI) 285, 370
RSP_0354 RSP_0354 hypothetical protein (NCBI) 242, 285
RSP_0424 RSP_0424 hypothetical protein (NCBI) 216, 285
RSP_0581 RSP_0581 hypothetical protein (NCBI) 157, 163
RSP_0595 RSP_0595 hypothetical protein (NCBI) 285, 329
RSP_0606 RSP_0606 Putative redox protein (NCBI) 97, 285
RSP_0709 cpdB 2',3'-cyclic-nucleotide 2'-phosphodiesterase (NCBI) 285, 329
RSP_0813 RSP_0813 Response regulator receiver protein (NCBI) 29, 157
RSP_0985 RSP_0985 adenine deaminase (NCBI) 285, 329
RSP_1000 RSP_1000 hypothetical protein (NCBI) 2, 285
RSP_1067 fixR Short-chain alcohol dehydrogenase (NCBI) 39, 285
RSP_1083 RSP_1083 two component transcriptional regulator, winged helix family (NCBI) 285, 329
RSP_1213 RSP_1213 hypothetical protein (NCBI) 157, 293
RSP_1297 RSP_1297 transcriptional regulator, LysR family (NCBI) 171, 285
RSP_1393 thiQ ABC thiamine transporter, ATPase subunit (NCBI) 31, 157
RSP_1405 RSP_1405 ROK family protein (NCBI) 285, 381
RSP_1432 RSP_1432 hypothetical protein (NCBI) 94, 157
RSP_1433 RSP_1433 hypothetical protein (NCBI) 141, 285
RSP_1527 RSP_1527 Helicase, UvrD/Rep family (NCBI) 110, 157
RSP_1778 RSP_1778 TPR domain protein (NCBI) 68, 285
RSP_1779 ispE Putative 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (NCBI) 68, 285
RSP_1780 RSP_1780 hypothetical protein (NCBI) 285, 323
RSP_1966 RSP_1966 possible ISSod13, transposase (NCBI) 19, 285
RSP_2003 yibQ YibQ protein (NCBI) 176, 285
RSP_2122 mtbC Putative dimethylamine corrinoid protein (NCBI) 185, 285
RSP_2396 RSP_2396 hypothetical protein (NCBI) 196, 285
RSP_2433 cheY2 Chemotaxis response regulator, CheY2 (NCBI) 285, 370
RSP_2553 RSP_2553 hypothetical protein (NCBI) 141, 157
RSP_2555 RSP_2555 hypothetical protein (NCBI) 77, 157
RSP_2556 RSP_2556 hypothetical protein (NCBI) 77, 157
RSP_2557 asnB putative asparagine synthetase (NCBI) 157, 323
RSP_2558 RSP_2558 hypothetical protein (NCBI) 157, 316
RSP_2588 RSP_2588 hypothetical protein (NCBI) 157, 363
RSP_2649 RSP_2649 Putative Zn-dependent protease (NCBI) 62, 285
RSP_2674 RSP_2674 hypothetical protein (NCBI) 48, 285
RSP_2731 ArsH arsenical resistance protein, ArsH (NCBI) 285, 313
RSP_2765 RSP_2765 hypothetical protein (NCBI) 88, 285
RSP_3029 RSP_3029 transcriptional regulator, GntR family (NCBI) 97, 157
RSP_3031 RSP_3031 ABC peptide/opine transporter, inner membrane subunit (NCBI) 97, 157
RSP_3085 RSP_3085 Conserved hypothetical membrane protein (NCBI) 157, 176
RSP_3109 RSP_3109 transcriptional regulator, MarR family (NCBI) 62, 285
RSP_3111 RSP_3111 Putative Glutathione S-transferase (NCBI) 62, 285
RSP_3112 RSP_3112 hypothetical protein (NCBI) 62, 285
RSP_3218 RSP_3218 Putative oxidoreductase NAD protein (NCBI) 112, 285
RSP_3253 RSP_3253 Predicted acetamidase / formamidase (NCBI) 157, 245
RSP_3255 RSP_3255 ABC peptide transporter, periplasmic binding protein (NCBI) 157, 245
RSP_3260 amiC Putative negative amidase regulator, AmiC (NCBI) 285, 325
RSP_3424 RSP_3424 hypothetical protein (NCBI) 38, 285
RSP_3655 RSP_3655 Dihydrodipicolinate synthase/N-acetylneuraminate lyase (NCBI) 105, 157
RSP_3700 RSP_3700 transcriptional regulator, LacI family (NCBI) 157, 251
RSP_3701 RSP_3701 ABC sugar transporter, periplasmic binding protein (NCBI) 157, 251
RSP_3702 RSP_3702 ABC sugar transporter, ATPase subunit (NCBI) 157, 251
RSP_3703 RSP_3703 ABC sugar transporter, inner membrane subunit (NCBI) 157, 251
RSP_3704 RSP_3704 ribitol 2-dehydrogenase (NCBI) 157, 251
RSP_3705 RSP_3705 D-ribulokinase (NCBI) 157, 251
RSP_3787 RSP_3787 hypothetical protein (NCBI) 236, 285
RSP_3797 RSP_3797 hypothetical protein (NCBI) 141, 157
RSP_3805 RSP_3805 possible integrase (NCBI) 157, 285
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 RSP_3805
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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