Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1260

hypothetical protein (NCBI)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1260
(Mouseover regulator name to see its description)

RSP_1260 is regulated by 32 influences and regulates 0 modules.
Regulators for RSP_1260 (32)
Regulator Module Operator
RSP_0601 286 tf
RSP_0607 286 tf
RSP_0958 286 tf
RSP_1034 286 tf
RSP_1274 286 tf
RSP_1892 286 tf
RSP_1922 286 tf
RSP_2130 286 tf
RSP_2201 286 tf
RSP_2610 286 tf
RSP_3324 286 tf
RSP_3464 286 tf
RSP_3680 286 tf
RSP_3748 286 tf
RSP_0014 207 tf
RSP_0087 207 tf
RSP_0327 207 tf
RSP_1220 207 tf
RSP_1231 207 tf
RSP_1243 207 tf
RSP_1297 207 tf
RSP_1550 207 tf
RSP_1606 207 tf
RSP_1607 207 tf
RSP_2591 207 tf
RSP_2610 207 tf
RSP_2838 207 tf
RSP_2922 207 tf
RSP_3029 207 tf
RSP_3124 207 tf
RSP_3203 207 tf
RSP_3514 207 tf

Warning: RSP_1260 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
8134 5.00e+02 CAgGgggaAG
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8135 7.00e+00 GAAAgGc.accggcGccg
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8286 1.30e+00 cgaaggTcaGgcAaagGatcg
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8287 4.00e+02 GtCgTTTcaaaCattTcGcGG
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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_1260

Warning: No Functional annotations were found!

Module neighborhood information for RSP_1260

RSP_1260 has total of 49 gene neighbors in modules 207, 286
Gene neighbors (49)
Gene Common Name Description Module membership
RSP_0024 rfbC Putative dTDP-4-dehydrorhamnose 3,5-epimerase (dTDP-L-rhamnose synthetase) (NCBI) 162, 207
RSP_0339 RSP_0339 hypothetical protein (NCBI) 280, 286
RSP_0412 RSP_0412 putative phosphatase (NCBI) 207, 308
RSP_0671 RSP_0671 ExbD/TolR family protein (NCBI) 286, 294
RSP_0672 TolQ Biopolymer transport protein, TolQ (NCBI) 277, 286
RSP_0758 RSP_0758 Lumazine-binding protein (NCBI) 127, 207
RSP_0799 RSP_0799 hypothetical protein (NCBI) 286, 287
RSP_0809 RSP_0809 hypothetical protein (NCBI) 67, 207
RSP_0810 RSP_0810 conserved hypothetical membrane protein (NCBI) 16, 207
RSP_0811 RSP_0811 hypothetical protein (NCBI) 173, 207
RSP_0871 patB putative aminotransferase (NCBI) 162, 207
RSP_0886 TyrB Aminotransferase (NCBI) 52, 207
RSP_0923 map1 Methionine aminopeptidase, subfamily 1 (NCBI) 84, 286
RSP_0924 cinA Predicted nucleotide-utilizing enzyme/competence-damage associated protein (NCBI) 71, 286
RSP_0925 yobR Putative acetyl transferase (NCBI) 84, 286
RSP_0926 RSP_0926 OmpA/MotB family protein (NCBI) 84, 286
RSP_0958 RSP_0958 RAM domain protein (NCBI) 82, 286
RSP_1260 RSP_1260 hypothetical protein (NCBI) 207, 286
RSP_1367 RSP_1367 Nicotinate phosphoribosyltransferase (NCBI) 207, 384
RSP_1401 RSP_1401 Band 7 protein (NCBI) 207, 294
RSP_1421 RSP_1421 hypothetical protein (NCBI) 286, 366
RSP_1542 RSP_1542 ABC transporter, ATPase subunit (NCBI) 210, 286
RSP_1594 cdd Cytidine deaminase (NCBI) 15, 207
RSP_1672 pdxJ PNP synthase, pyridoxal phosphate biosynthetic protein PdxJ (NCBI) 181, 286
RSP_1756 panB probable 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI) 52, 207
RSP_1757 panC Probable pantoate--beta-alanine ligase (NCBI) 207, 278
RSP_1956 RSP_1956 hypothetical protein (NCBI) 280, 286
RSP_2000 RSP_2000 molybdenum cofactor biosynthesis protein C (NCBI) 30, 207
RSP_2001 trpD Anthranilate phosphoribosyltransferase (NCBI) 52, 207
RSP_2002 trpG Anthranilate synthase component II (NCBI) 52, 207
RSP_2091 RSP_2091 Putative benzoate transporter, BenE (NCBI) 184, 207
RSP_2106 ftsW cell division protein FtsW (NCBI) 207, 349
RSP_2201 RSP_2201 transcriptional regulator, MerR family (NCBI) 162, 286
RSP_2216 ilvE Aminotransferase, class IV (NCBI) 127, 207
RSP_2330 leuA 2-Isopropylmalate synthase (NCBI) 185, 286
RSP_2374 RSP_2374 hypothetical protein (NCBI) 218, 286
RSP_2387 RSP_2387 hypothetical protein (NCBI) 71, 286
RSP_2643 glnE Glutamate-ammonia-ligase adenylyltransferase (NCBI) 121, 207
RSP_2644 RSP_2644 hypothetical protein (NCBI) 121, 207
RSP_2646 RSP_2646 None 286, 309
RSP_2695 RSP_2695 Possible peptidoglycan binding protein (NCBI) 81, 207
RSP_2846 RSP_2846 putative 3-hydroxyisobutyrate dehydrogenase (NCBI) 81, 207
RSP_2862 RSP_2862 Glycine/D-amino acid oxidases (deaminating) (NCBI) 127, 207
RSP_2969 RSP_2969 hypothetical protein (NCBI) 127, 207
RSP_2973 RSP_2973 Peroxiredoxin (NCBI) 158, 286
RSP_3069 RSP_3069 NADPH-dependent FMN reductase (NCBI) 81, 207
RSP_3324 RSP_3324 transcriptional regulator, LuxR family (NCBI) 46, 286
RSP_3563 RSP_3563 putative FAD-dependent glycerol-3-phosphate dehydrogenase protein (NCBI) 127, 207
RSP_3730 RSP_3730 putative glutathione S-transferase (NCBI) 81, 207
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_1260
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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