Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3635

putative adenine-specific DNA methyltransferase (NCBI)

CircVis
Functional Annotations (5)
Function System
Site-specific DNA methylase cog/ cog
DNA binding go/ molecular_function
DNA methylation go/ biological_process
site-specific DNA-methyltransferase (adenine-specific) activity go/ molecular_function
Mismatch repair kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3635
(Mouseover regulator name to see its description)

RSP_3635 is regulated by 22 influences and regulates 0 modules.
Regulators for RSP_3635 (22)
Regulator Module Operator
RSP_1231 379 tf
RSP_1590 379 tf
RSP_1607 379 tf
RSP_1612 379 tf
RSP_1660 379 tf
RSP_1776 379 tf
RSP_1790 379 tf
RSP_1871 379 tf
RSP_2026 379 tf
RSP_2867 379 tf
RSP_3322 379 tf
RSP_3464 379 tf
RSP_3684 379 tf
RSP_0386 355 tf
RSP_0394 355 tf
RSP_1272 355 tf
RSP_1274 355 tf
RSP_2867 355 tf
RSP_2922 355 tf
RSP_3064 355 tf
RSP_3464 355 tf
RSP_3684 355 tf

Warning: RSP_3635 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
8408 8.40e+02 aaAgcaaGtgtcAacaTgct
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8409 2.90e+02 aTttc.cgCttcGaT
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8448 3.00e-21 TCgCcgttcgagACgAGgAgcTCc
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8449 1.80e-19 AaCAGcCCGAaCcaCcccGCC
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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_3635

RSP_3635 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Site-specific DNA methylase cog/ cog
DNA binding go/ molecular_function
DNA methylation go/ biological_process
site-specific DNA-methyltransferase (adenine-specific) activity go/ molecular_function
Mismatch repair kegg/ kegg pathway
Module neighborhood information for RSP_3635

RSP_3635 has total of 45 gene neighbors in modules 355, 379
Gene neighbors (45)
Gene Common Name Description Module membership
RSP_1084 RSP_1084 putative glycosyl transferase, group 1 family protein (NCBI) 325, 379
RSP_1170 RSP_1170 OmpA family protein (NCBI) 267, 355
RSP_1205 RSP_1205 Poly A polymerase family protein (NCBI) 6, 355
RSP_1436 RSP_1436 ABC transporter, duplicated ATPase domains (NCBI) 150, 379
RSP_1533 RSP_1533 putative alginate O-acetyltransferase (NCBI) 101, 355
RSP_1534 RSP_1534 putative acyl carrier protein (NCBI) 101, 355
RSP_1535 RSP_1535 hypothetical protein (NCBI) 101, 355
RSP_1612 RSP_1612 Sigma-54 dependent transcriptional regulator (NCBI) 370, 379
RSP_1625 RSP_1625 hypothetical protein (NCBI) 217, 379
RSP_1626 RSP_1626 hypothetical protein (NCBI) 217, 379
RSP_1627 RSP_1627 Putative N-6 adenine-specific DNA methylase (NCBI) 245, 379
RSP_1648 RSP_1648 hypothetical protein (NCBI) 193, 355
RSP_1649 RSP_1649 Possible transporter, DMT superfamily (NCBI) 188, 355
RSP_1753 RSP_1753 hypothetical protein (NCBI) 304, 355
RSP_1961 RSP_1961 hypothetical protein (NCBI) 235, 355
RSP_2049 RSP_2049 hypothetical protein (NCBI) 217, 379
RSP_2050 RSP_2050 hypothetical protein (NCBI) 217, 379
RSP_2052 RSP_2052 N6 adenine-specific DNA methyltransferase, D12 class (NCBI) 73, 379
RSP_2055 RSP_2055 hypothetical protein (NCBI) 103, 379
RSP_2061 RSP_2061 hypothetical protein (NCBI) 292, 379
RSP_2074 RSP_2074 hypothetical protein (NCBI) 38, 379
RSP_2076 RSP_2076 hypothetical protein (NCBI) 189, 355
RSP_2077 RSP_2077 hypothetical protein (NCBI) 313, 355
RSP_2078 RSP_2078 hypothetical protein (NCBI) 296, 355
RSP_2185 RSP_2185 nuclease (SNase-like) (NCBI) 220, 355
RSP_2349 RSP_2349 hypothetical protein (NCBI) 293, 355
RSP_2490 RSP_2490 hypothetical protein (NCBI) 220, 355
RSP_2500 RSP_2500 hypothetical protein (NCBI) 313, 355
RSP_2799 RSP_2799 Putative Zinc-containing alcohol dehydrogenase (NCBI) 62, 379
RSP_2992 RSP_2992 hypothetical protein (NCBI) 44, 355
RSP_2993 RSP_2993 hypothetical protein (NCBI) 19, 355
RSP_2994 RSP_2994 hypothetical protein (NCBI) 155, 355
RSP_3139 RSP_3139 hypothetical protein (NCBI) 313, 355
RSP_3389 RSP_3389 Isocitrate/isopropylmalate dehydrogenase / tartrate dehydrogenase (NCBI) 220, 355
RSP_3517 RSP_3517 ABC polyamine/opine transporter, inner membrane subunit (NCBI) 331, 379
RSP_3626 RSP_3626 None 19, 379
RSP_3627 RSP_3627 Periplasmic serine proteases (NCBI) 73, 379
RSP_3634 RSP_3634 hypothetical protein (NCBI) 48, 379
RSP_3635 RSP_3635 putative adenine-specific DNA methyltransferase (NCBI) 355, 379
RSP_3636 RSP_3636 hypothetical protein (NCBI) 217, 379
RSP_3637 RSP_3637 hypothetical protein (NCBI) 217, 379
RSP_3639 RSP_3639 hypothetical protein (NCBI) 313, 355
RSP_3760 RSP_3760 hypothetical protein (NCBI) 217, 379
RSP_3761 RSP_3761 hypothetical protein (NCBI) 217, 379
RSP_3769 RSP_3769 Adenine-specific DNA methyltransferase (NCBI) 245, 379
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_3635
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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