Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0627

Putative amidohydrolase (NCBI)

CircVis
Functional Annotations (5)
Function System
Predicted amidohydrolase cog/ cog
cysteine-type endopeptidase activity go/ molecular_function
proteolysis go/ biological_process
nitrogen compound metabolic process go/ biological_process
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0627
(Mouseover regulator name to see its description)

RSP_0627 is regulated by 28 influences and regulates 0 modules.
Regulators for RSP_0627 (28)
Regulator Module Operator
RSP_0386 159 tf
RSP_0443 159 tf
RSP_0601 159 tf
RSP_0755 159 tf
RSP_1663 159 tf
RSP_1741 159 tf
RSP_1892 159 tf
RSP_2346 159 tf
RSP_2533 159 tf
RSP_2838 159 tf
RSP_2850 159 tf
RSP_2922 159 tf
RSP_3700 159 tf
RSP_0728 190 tf
RSP_0755 190 tf
RSP_1286 190 tf
RSP_1712 190 tf
RSP_2165 190 tf
RSP_2346 190 tf
RSP_2572 190 tf
RSP_2801 190 tf
RSP_2838 190 tf
RSP_2850 190 tf
RSP_2965 190 tf
RSP_3001 190 tf
RSP_3226 190 tf
RSP_3322 190 tf
RSP_3664 190 tf

Warning: RSP_0627 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
8038 3.20e-69 GATAtTTgggCCAGAaTGAAaG
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8039 1.30e-17 cGGGggtCgGGGGGCAGac.cCCC
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8100 2.60e-60 cactctGc.cAAATATCCTCGGGG
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8101 3.00e-28 CgGGGGGCaGACAGCCCCCcG
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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_0627

RSP_0627 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted amidohydrolase cog/ cog
cysteine-type endopeptidase activity go/ molecular_function
proteolysis go/ biological_process
nitrogen compound metabolic process go/ biological_process
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds go/ molecular_function
Module neighborhood information for RSP_0627

RSP_0627 has total of 46 gene neighbors in modules 159, 190
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0006 RSP_0006 possible transporter, DMT superfamily (NCBI) 159, 190
RSP_0007 RSP_0007 putative outer membrane protein (NCBI) 190, 248
RSP_0183 dht phenylhydantoinase (RefSeq) 156, 190
RSP_0389 folA Dihydrofolate reductase (NCBI) 159, 248
RSP_0390 RSP_0390 Thymidylate synthase (NCBI) 159, 248
RSP_0395 rpoD RNA polymerase sigma factor RpoD (NCBI) 159, 248
RSP_0396 RSP_0396 hypothetical protein (NCBI) 159, 248
RSP_0397 dnaG DNA primase (DnaG) (NCBI) 159, 248
RSP_0442 RSP_0442 putative aminotransferase (NCBI) 159, 161
RSP_0447 RSP_0447 hypothetical protein (NCBI) 159, 248
RSP_0597 RSP_0597 Probable molybdopterin biosynthesis protein (NCBI) 159, 248
RSP_0598 RSP_0598 Probable deoxyuridine-triphosphatase (NCBI) 159, 248
RSP_0627 RSP_0627 Putative amidohydrolase (NCBI) 159, 190
RSP_0628 RSP_0628 hypothetical protein (NCBI) 159, 190
RSP_0629 RSP_0629 hypothetical protein (NCBI) 159, 190
RSP_0630 RSP_0630 hypothetical protein (NCBI) 159, 190
RSP_0631 RSP_0631 hypothetical protein (NCBI) 159, 190
RSP_0632 hisD1 Histidinol dehydrogenase (NCBI) 159, 190
RSP_0776 LolD ABC lipoprotein efflux transporter, ATPase subunit, LolD (NCBI) 159, 190
RSP_0777 LolE ABC lipoprotein efflux transporter, inner membrane subunit, LolE (NCBI) 159, 190
RSP_0962 RSP_0962 Dihydrolipoamide dehydrogenase (NCBI) 190, 208
RSP_1046 RSP_1046 hypothetical protein (NCBI) 156, 190
RSP_1125 MltB Membrane bound lytic murein transglycosylase B (NCBI) 156, 190
RSP_1552 RSP_1552 putative ureidoglycolate hydrolase (NCBI) 156, 190
RSP_1697 RSP_1697 hypothetical protein (NCBI) 156, 190
RSP_1841 RSP_1841 Probable intracellular septation protein (NCBI) 156, 190
RSP_1842 RSP_1842 possible transporter, DME family, DMT superfamily (NCBI) 156, 190
RSP_2137 RSP_2137 hypothetical protein (NCBI) 156, 190
RSP_2138 fumC Fumarate lyase (NCBI) 156, 190
RSP_2143 RSP_2143 DNA photolyase, Cryptochrome 1 apoprotein (Blue light photoreceptor) (NCBI) 159, 190
RSP_2212 rimI putative acetyltransferase (NCBI) 159, 267
RSP_2213 RSP_2213 hypothetical protein (NCBI) 159, 265
RSP_2340 RSP_2340 MiaB-like Radical SAM protein (NCBI) 159, 248
RSP_2723 RSP_2723 Isopropylmalate/homocitrate/citramalate synthases (NCBI) 156, 159
RSP_2724 RSP_2724 Probable Methylase involved in ubiquinone/menaquinone biosynthesis (NCBI) 156, 159
RSP_2725 RSP_2725 Probable Phytoene/squalene synthetase (NCBI) 156, 159
RSP_2804 tgt Probable queuine tRNA ribosyltransferase (NCBI) 190, 258
RSP_2906 RSP_2906 Putative methylase (NCBI) 159, 190
RSP_2978 mrcA Penicillin-binding protein 1A (PBP-1a) (NCBI) 159, 248
RSP_3596 lnt Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (NCBI) 156, 190
RSP_6054 RSP_6054 hypothetical protein (NCBI) 190, 194
RSP_6069 RSP_6069 hypothetical protein (NCBI) 190, 194
RSP_6152 RSP_6152 hypothetical protein (NCBI) 33, 190
RSP_6181 RSP_6181 None 190, 248
RSP_6188 RSP_6188 hypothetical protein (NCBI) 190, 194
RSP_6242 RSP_6242 hypothetical protein (NCBI) 190, 194
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_0627
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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