Organism : Methanococcus maripaludis S2 | Module List :
MMP0607 nrpR

hypothetical protein MMP0607

CircVis
Functional Annotations (1)
Function System
Uncharacterized protein conserved in archaea cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0607
(Mouseover regulator name to see its description)

MMP0607 is regulated by 2 influences and regulates 9 modules.
Regulators for MMP0607 nrpR (2)
Regulator Module Operator
MMP0033
MMP0168
115 combiner
H2 137 ef

Warning: MMP0607 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
887 3.20e+02 tT.AaaagGGg.AAc
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888 2.00e+03 ACAaTActGC
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925 2.30e+03 GTTCGATtg.g..TCT.g.ctC
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926 5.30e+03 AAACaAtGtTTtattaTacg
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937 2.40e+03 GAGcGCCC
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938 4.70e+03 ccca.CAatTc.gc.AtaT
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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 MMP0607

MMP0607 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Uncharacterized protein conserved in archaea cog/ cog
Module neighborhood information for MMP0607

MMP0607 has total of 67 gene neighbors in modules 115, 137, 143
Gene neighbors (67)
Gene Common Name Description Module membership
MMP0007 geranylgeranylglyceryl phosphate synthase-like protein 12, 143
MMP0038 type II secretion system protein 115, 160
MMP0039 hypothetical protein MMP0039 115, 160
MMP0040 type II secretion system protein E 115, 160
MMP0118 beta-lactamase domain-containing protein 115, 133
MMP0145 hpt adenine phosphoribosyltransferase 137, 143
MMP0146 hypothetical protein MMP0146 17, 41, 137
MMP0153 aksA trans-homoaconitate synthase 1, 143
MMP0165 ABC transporter 28, 115
MMP0178 purQ phosphoribosylformylglycinamidine synthase I 95, 143
MMP0179 purL phosphoribosylformylglycinamidine synthase 66, 143
MMP0187 thiC thiamine biosynthesis protein ThiC 137, 143
MMP0233 hypothetical protein MMP0233 38, 115
MMP0264 MscMJ mechanosensitive ion channel MscS 129, 143
MMP0403 hypothetical protein MMP0403 87, 115
MMP0404 cofD 2-phospho-L-lactate transferase 87, 137
MMP0417 hisA 1-(5-phosphoribosyl)-5- 60, 137
MMP0418 carbohydrate kinase PfkB 60, 137, 143
MMP0540 purC phosphoribosylaminoimidazole-succinocarboxamide synthase 8, 112, 143
MMP0579 hypothetical protein MMP0579 115, 139
MMP0580 act anaerobic ribonucleoside-triphosphate reductase activating protein 115, 129
MMP0606 ribosomal RNA methyltransferase RrmJ/FtsJ 137, 143
MMP0607 nrpR hypothetical protein MMP0607 115, 137, 143
MMP0632 ATP/GTP-binding motif-containing protein 19, 115
MMP0666 Na/Pi-cotransporter II-like protein 7, 115
MMP0689 xanthine/uracil permease family protein 38, 115
MMP0697 leuS leucyl-tRNA synthetase 8, 143
MMP0698 hypothetical protein MMP0698 21, 143
MMP0865 aminotransferase (subgroup II) adenosylmethionine-8-amino-7-oxononanoate aminotransferase 115, 140
MMP0879 serS seryl-tRNA synthetase 27, 143
MMP0880 aksF isopropylmalate/isohomocitrate dehydrogenase 24, 60, 140, 143
MMP0881 hypothetical protein MMP0881 111, 137
MMP0883 hypothetical protein MMP0883 115, 129
MMP0918 asnB glutamine-hydrolyzing asparagine synthase 49, 115
MMP0942 hypothetical protein MMP0942 111, 115
MMP0948 hypothetical protein MMP0948 4, 115
MMP0969 hypothetical protein MMP0969 106, 115
MMP1063 leuA 2-isopropylmalate synthase 81, 143
MMP1069 basic helix-loop-helix dimerization domain-containing protein 106, 115
MMP1081 wbpG putative LPS biosynthesis protein WbpG 137, 143
MMP1082 hisH imidazole glycerol phosphate synthase subunit HisH 66, 143
MMP1083 imidazole glycerol phosphate synthase subunit HisF 137, 143
MMP1085 hypothetical protein MMP1085 141, 143, 149
MMP1105 sucC succinate-CoA ligase (ADP-forming), beta chain 7, 81, 137
MMP1106 hypothetical protein MMP1106 81, 137, 140
MMP1122 translation-associated GTPase 137, 143
MMP1146 purF amidophosphoribosyltransferase 7, 60, 137, 143
MMP1186 lon thiol (cysteine) protease 21, 115
MMP1198 nitrate/sulfonate/bicarbonate ABC transporter ATPase 12, 143
MMP1206 glnA glutamine synthetase 99, 137
MMP1279 camphor resistance protein CrcB 115, 160
MMP1290 GTP-binding protein 49, 115
MMP1316 korB 2-oxoglutarate ferredoxin oxidoreductase subunit beta 7, 120, 137
MMP1317 hypothetical protein MMP1317 21, 115
MMP1430 cation transporter 49, 115
MMP1440 tRNA-modifying protein 129, 137
MMP1471 hypothetical protein MMP1471 38, 115
MMP1496 pheS phenylalanyl-tRNA synthetase subunit alpha 137, 143
MMP1532 pgk phosphoglycerate kinase 120, 137
MMP1592 trpS tryptophanyl-tRNA synthetase 27, 143
MMP1594 hypothetical protein MMP1594 51, 143
MMP1656 glutamine amidotransferase subunit PdxT 8, 137
MMP1681 hypothetical protein MMP1681 21, 143
MMP1704 hypothetical protein MMP1704 21, 115
MMP1711 pcnA proliferating cell nuclear antigen 115, 139
MMP1722 hisF imidazole glycerol phosphate synthase subunit HisF 111, 115
Unanno_24 None 95, 143
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 MMP0607
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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