Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3758

Cytosine-specific DNA methylase (NCBI)

CircVis
Functional Annotations (9)
Function System
Site-specific DNA methylase cog/ cog
DNA binding go/ molecular_function
DNA methylation go/ biological_process
DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates go/ molecular_function
DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates go/ molecular_function
DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
dcm tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3758
(Mouseover regulator name to see its description)

RSP_3758 is regulated by 38 influences and regulates 0 modules.
Regulators for RSP_3758 (38)
Regulator Module Operator
RSP_0014 130 tf
RSP_0386 130 tf
RSP_0395 130 tf
RSP_0623 130 tf
RSP_0722 130 tf
RSP_0760 130 tf
RSP_0907 130 tf
RSP_1164 130 tf
RSP_1220 130 tf
RSP_1225 130 tf
RSP_1712 130 tf
RSP_1741 130 tf
RSP_1890 130 tf
RSP_1922 130 tf
RSP_2182 130 tf
RSP_2681 130 tf
RSP_2801 130 tf
RSP_2838 130 tf
RSP_2840 130 tf
RSP_2950 130 tf
RSP_2965 130 tf
RSP_3436 130 tf
RSP_3665 130 tf
RSP_0032 57 tf
RSP_0601 57 tf
RSP_0768 57 tf
RSP_0927 57 tf
RSP_1669 57 tf
RSP_1866 57 tf
RSP_1952 57 tf
RSP_2130 57 tf
RSP_2171 57 tf
RSP_2591 57 tf
RSP_2681 57 tf
RSP_2730 57 tf
RSP_2939 57 tf
RSP_3324 57 tf
RSP_3620 57 tf

Warning: RSP_3758 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
7834 6.30e-08 aaaAAAtCgG
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7835 5.90e+00 ATCTATGCCCTTTGTGATATATA
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7980 1.60e-01 T.ttgGCtTGAaga.caggg
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7981 9.70e+03 Aa.AA.gAaaa
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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_3758

RSP_3758 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Site-specific DNA methylase cog/ cog
DNA binding go/ molecular_function
DNA methylation go/ biological_process
DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates go/ molecular_function
DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates go/ molecular_function
DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates go/ molecular_function
Cysteine and methionine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
dcm tigr/ tigrfam
Module neighborhood information for RSP_3758

RSP_3758 has total of 53 gene neighbors in modules 57, 130
Gene neighbors (53)
Gene Common Name Description Module membership
RSP_0341 RSP_0341 Cytosine deaminase (NCBI) 57, 114
RSP_0342 RSP_0342 putative ABC sugar transporter, inner membrane subunit (NCBI) 57, 114
RSP_0343 RSP_0343 putative ABC sugar transporter, inner membrane subunit (NCBI) 57, 204
RSP_0344 RSP_0344 putative ABC sugar transporter, fused ATPase subunits (NCBI) 57, 204
RSP_0347 RSP_0347 ABC transporter, inner membrane subunit (NCBI) 57, 204
RSP_0348 RSP_0348 ABC transporter, inner membrane subunit (NCBI) 57, 204
RSP_0445 RSP_0445 hypothetical protein (NCBI) 47, 130
RSP_0651 RSP_0651 Putative inositol monophosphatase protein (NCBI) 33, 130
RSP_0652 RSP_0652 UDP-glucose 4-epimerase (NCBI) 130, 374
RSP_0656 RSP_0656 Probable sodium/sulphate symporter (NCBI) 130, 293
RSP_0677 RSP_0677 Putative malonate transporter, mdcF, AEC family (NCBI) 130, 221
RSP_0702 RSP_0702 ABC peptide transporter, inner membrane subunit (NCBI) 130, 374
RSP_0703 RSP_0703 ABC peptide transporter, inner membrane subunit (NCBI) 130, 374
RSP_0781 RSP_0781 polyphosphate kinase (NCBI) 130, 374
RSP_0805 DppC ABC dipeptide transporter, inner membrane subunit DppC (NCBI) 57, 67
RSP_0889 glnK Nitrogen regulatory protein P-II (NCBI) 57, 358
RSP_0930 folC Folylpolyglutamate synthetase (NCBI) 130, 277
RSP_1049 pheAa putative chorismate mutase protein (NCBI) 47, 130
RSP_1065 RSP_1065 hypothetical protein (NCBI) 130, 209
RSP_1066 RSP_1066 Probable GTP-binding protein (NCBI) 5, 130
RSP_1156 RSP_1156 ABC transporter, ATPase subunit (NCBI) 47, 130
RSP_1289 RSP_1289 ABC branched chain amino acid family transporter, inner membrane subunit (NCBI) 130, 263
RSP_1569 RSP_1569 probable aminotransferase (NCBI) 130, 374
RSP_1623 RSP_1623 hypothetical protein (NCBI) 93, 130
RSP_1670 spoT/relA RelA/SpoT family protein (NCBI) 130, 383
RSP_2090 pycA Pyruvate carboxylase (NCBI) 16, 57
RSP_2158 RSP_2158 ABC transporter, periplasmic solute-binding protein (NCBI) 57, 59
RSP_2190 RSP_2190 hypothetical protein (NCBI) 65, 130
RSP_2458 RSP_2458 ABC transporter, ATPase subunit (NCBI) 87, 130
RSP_2542 RSP_2542 ATPase (NCBI) 130, 372
RSP_2707 uppS Undecaprenyl pyrophosphate synthase (NCBI) 130, 374
RSP_2708 cdsA Phosphatidate cytidylyltransferase (NCBI) 130, 374
RSP_2904 pdxA1 Putative4-hydroxythreonine-4-phosphate dehydrogenase 1 (NCBI) 87, 130
RSP_3037 RSP_3037 Putative short-chain dehydrogenase/reductase (NCBI) 57, 168
RSP_3038 RSP_3038 ABC permidine/putrescine transporter, inner membrane subunit (NCBI) 57, 106
RSP_3039 RSP_3039 ABC permidine/putrescine transporter, inner membrane subunit (NCBI) 57, 106
RSP_3040 RSP_3040 ABC permidine/putrescine transporter, periplasmic substrate-binding protein (NCBI) 57, 106
RSP_3041 RSP_3041 ABC permidine/putrescine transporter, ATPase subunit (NCBI) 57, 106
RSP_3042 dorX DMSO reductase regulatory protein DorX (NCBI) 57, 106
RSP_3136 RSP_3136 hypothetical protein (NCBI) 88, 130
RSP_3248 RSP_3248 ABC peptide transporter, periplasmic binding protein (NCBI) 57, 114
RSP_3381 RSP_3381 NAD(P)H -dependent quinone oxidoreductase (NCBI) 57, 175
RSP_3382 RSP_3382 hypothetical protein (NCBI) 57, 102
RSP_3383 RSP_3383 hypothetical protein (NCBI) 57, 102
RSP_3513 RSP_3513 GAF sensor diguanylate cyclase (NCBI) 57, 293
RSP_3644 RSP_3644 Metal dependent phosphohydrolase (NCBI) 93, 130
RSP_3645 RSP_3645 hypothetical protein (NCBI) 65, 130
RSP_3687 RSP_3687 ABC sugar transporter, periplasmic binding protein (NCBI) 57, 171
RSP_3688 RSP_3688 ABC sugar transporter, ATPase subunit (NCBI) 57, 171
RSP_3689 yphD ABC sugar transporter, inner membrane subunit (NCBI) 57, 88
RSP_3691 RSP_3691 putative cytoplasmic protein (NCBI) 31, 57
RSP_3758 RSP_3758 Cytosine-specific DNA methylase (NCBI) 57, 130
RSP_3759 RSP_3759 Putative endonuclease (NCBI) 130, 175
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_3758
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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