Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1970

Phosphoribosylglycinamide formyltransferase (NCBI)

CircVis
Functional Annotations (9)
Function System
Folate-dependent phosphoribosylglycinamide formyltransferase PurN cog/ cog
phosphoribosylglycinamide formyltransferase activity go/ molecular_function
'de novo' IMP biosynthetic process go/ biological_process
translation go/ biological_process
Purine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
PurN tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1970
(Mouseover regulator name to see its description)

RSP_1970 is regulated by 16 influences and regulates 0 modules.
Regulators for RSP_1970 (16)
Regulator Module Operator
RSP_0386 84 tf
RSP_0755 84 tf
RSP_1660 84 tf
RSP_3238 84 tf
RSP_3341 84 tf
RSP_0386 209 tf
RSP_0395 209 tf
RSP_0547 209 tf
RSP_0623 209 tf
RSP_1164 209 tf
RSP_1191 209 tf
RSP_1220 209 tf
RSP_1866 209 tf
RSP_1892 209 tf
RSP_2324 209 tf
RSP_3202 209 tf

Warning: RSP_1970 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
7888 1.20e-01 aGAtCGgTCAgCTtccGccCCcG
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7889 9.10e+00 CcgAAGGcTcG.aacaaccCGCGg
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8138 2.20e-06 AAcAa.AcTATA.TCtgT
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8139 5.20e+00 aaAtaGGCGaacaTGaCtCGGACG
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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_1970

RSP_1970 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Folate-dependent phosphoribosylglycinamide formyltransferase PurN cog/ cog
phosphoribosylglycinamide formyltransferase activity go/ molecular_function
'de novo' IMP biosynthetic process go/ biological_process
translation go/ biological_process
Purine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
PurN tigr/ tigrfam
Module neighborhood information for RSP_1970

RSP_1970 has total of 53 gene neighbors in modules 84, 209
Gene neighbors (53)
Gene Common Name Description Module membership
RSP_0448 RSP_0448 EF-Tu; elongation factor Tu (NCBI) 209, 271
RSP_0684 RSP_0684 Possible oxidoreductase; Short-chain dehydrogenase/reductase SDR (NCBI) 196, 209
RSP_0685 RSP_0685 Possible ribosomal RNA small subunit methyltransferase C RsmC (NCBI) 209, 340
RSP_0686 RSP_0686 ATP-dependent Clp protease adaptor protein clpS (NCBI) 209, 227
RSP_0687 RSP_0687 Predicted hydrolase (haloacid dehalogenase (HAD) superfamily) (NCBI) 192, 209
RSP_0818 carB carbamoyl phosphate synthase large subunit (RefSeq) 209, 383
RSP_0819 rhlE2 DEAD/DEAH box helicase (NCBI) 209, 316
RSP_0923 map1 Methionine aminopeptidase, subfamily 1 (NCBI) 84, 286
RSP_0925 yobR Putative acetyl transferase (NCBI) 84, 286
RSP_0926 RSP_0926 OmpA/MotB family protein (NCBI) 84, 286
RSP_0987 RSP_0987 Putative transporter, RarD family, DMT superfamily (NCBI) 84, 126
RSP_1062 RSP_1062 ATPases of the PP superfamily (NCBI) 110, 209
RSP_1065 RSP_1065 hypothetical protein (NCBI) 130, 209
RSP_1075 RSP_1075 Short-chain dehydrogenase/reductase SDR (NCBI) 209, 218
RSP_1108 TruB tRNA pseudouridine synthase B (NCBI) 209, 383
RSP_1110 RSP_1110 hypothetical protein (NCBI) 209, 271
RSP_1197 HemH Ferrochelatase (NCBI) 209, 311
RSP_1202 TrmA putative RNA SAM-dependent methyltransferase, TrmA family (NCBI) 47, 209
RSP_1203 RSP_1203 ABC multidrug efflux pump, fused ATPase and inner membrane subunits (NCBI) 196, 209
RSP_1218 mutS DNA mismatch repair protein MutS (NCBI) 209, 299
RSP_1263 RSP_1263 hypothetical protein (NCBI) 84, 307
RSP_1264 RSP_1264 hypothetical protein (NCBI) 84, 307
RSP_1265 kdpA Potassium-transporting P-type ATPase, A chain, KdpA (NCBI) 84, 307
RSP_1266 kdpB Potassium-transporting P-type ATPase, B chain, KdpB (NCBI) 84, 307
RSP_1267 kdpC Potassium-transporting P-type ATPase C chain, kdpC (NCBI) 84, 307
RSP_1268 kdpD Osmosensitive K+ channel histidine kinase (NCBI) 84, 307
RSP_1269 kdpE two component transcriptional regulator, winged helix family (NCBI) 84, 307
RSP_1339 RSP_1339 Formamidopyrimidine-DNA glycolase (NCBI) 84, 331
RSP_1426 RSP_1426 RNA-binding region RNP-1 (NCBI) 209, 316
RSP_1427 RSP_1427 hypothetical protein (NCBI) 209, 316
RSP_1462 lpxK Putative Tetraacyldisaccharide-1-P 4'-kinase (NCBI) 84, 234
RSP_1470 rnhB ribonuclease HII (NCBI) 84, 164
RSP_1484 RSP_1484 hypothetical protein (NCBI) 209, 268
RSP_1485 RSP_1485 ATP-dependent RNA helicase (NCBI) 209, 268
RSP_1799 secF protein-export membrane protein SecF (NCBI) 209, 224
RSP_1970 RSP_1970 Phosphoribosylglycinamide formyltransferase (NCBI) 84, 209
RSP_2118 recN DNA repair protein RecN (NCBI) 209, 339
RSP_2534 RSP_2534 Predicted hydrolase of the metallo-beta-lactamase superfamily (NCBI) 84, 361
RSP_2552 exoU Glycosyl transferase, family 2 (NCBI) 209, 316
RSP_2599 phoB Phosphate regulon transcriptional regulator, PhoR (NCBI) 84, 155
RSP_2648 RSP_2648 hypothetical protein (NCBI) 209, 383
RSP_2790 RSP_2790 hypothetical protein (NCBI) 84, 356
RSP_2815 xerD Probable integrase/recombinase XerD (NCBI) 84, 326
RSP_2818 aroB Putative 3-dehydroquinate synthase (NCBI) 84, 234
RSP_3004 RSP_3004 Possible Protein kinase (NCBI) 209, 214
RSP_3091 RSP_3091 Coserved hypothetical protein (NCBI) 54, 84
RSP_3273 RSP_3273 ABC multidrug/carbohydrate efflux transporter, inner membrane subunit (NCBI) 116, 209
RSP_3274 RSP_3274 ABC multidrug/carbohydrate efflux transporter, ATPase subunit (NCBI) 116, 209
RSP_3448 RSP_3448 transcriptional regulator, GntR-family (NCBI) 84, 220
RSP_3449 RSP_3449 Putative allophanate hydrolase subunit 2 (NCBI) 61, 84
RSP_3450 RSP_3450 hypothetical protein (NCBI) 61, 84
RSP_3565 RSP_3565 Glycoside hydrolase, family 25 (NCBI) 84, 221
RSP_3591 RSP_3591 cytidylate kinase (NCBI) 209, 271
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_1970
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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