Organism : Methanococcus maripaludis S2 | Module List :
MMP1387

hypothetical protein MMP1387

CircVis
Functional Annotations (1)
Function System
Predicted dioxygenase cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1387
(Mouseover regulator name to see its description)

MMP1387 is regulated by 7 influences and regulates 0 modules.
Regulators for MMP1387 (7)
Regulator Module Operator
H2 33 ef
MMP0499 33 tf
MMP0499
MMP1065		 33 combiner
MMP0907
MMP1646		 33 combiner
MMP1015 33 tf
MMP0527
MMP1100		 150 combiner
MMP1376 150 tf

Warning: MMP1387 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
727 3.20e-01 TgTaaAtttgGgGGtGagA
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728 2.60e+02 CggAATCTAGC
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807 3.50e+02 TaTCAcCcCc
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808 1.40e+03 cacGGaactatTGgA
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949 5.10e+02 TacgGggtGtT
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950 2.10e+03 cttCatatt.cA.AatccccTTc
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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 MMP1387

MMP1387 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted dioxygenase cog/ cog
Module neighborhood information for MMP1387

MMP1387 has total of 45 gene neighbors in modules 33, 73, 150
Gene neighbors (45)
Gene Common Name Description Module membership
Antisense_10 None 2, 43, 150
MMP0069 methylated-DNA--protein-cysteine methyltransferase 23, 150
MMP0086 tfx putative transcriptional regulator 150, 160
MMP0102 pcm protein-L-isoaspartate O-methyltransferase 2, 43, 150
MMP0128 cyclase family protein 73, 146, 153
MMP0182 hypothetical protein MMP0182 2, 73
MMP0190 hypothetical protein MMP0190 150, 159
MMP0304 N-glycosylase/DNA lyase 22, 33, 43, 152
MMP0305 2-oxoacid ferredoxin oxidoreductase subunit beta 2, 33, 43
MMP0306 oxidoreductase family protein member subunit alpha 2, 33, 43
MMP0307 hypothetical protein MMP0307 33, 49, 153
MMP0311 hypothetical protein MMP0311 33, 73
MMP0312 hypothetical protein MMP0312 73, 94
MMP0313 hypothetical protein MMP0313 28, 73
MMP0456 xerD-like Phage integrase 73, 99
MMP0520 HAD superfamily ATPase 73, 146
MMP0528 hypothetical protein MMP0528 23, 150
MMP0559 hypothetical protein MMP0559 73, 156
MMP0599 cbiJ precorrin-6x reductase CbiJ/CobK 33, 152
MMP0600 hypothetical protein MMP0600 2, 33
MMP0678 hypothetical protein MMP0678 73, 76
MMP0691 hypothetical protein MMP0691 33, 73
MMP0693 aminoacyl-tRNA synthetase, class II 33, 54
MMP0848 peptide methionine sulfoxide reductase 73, 83
MMP0903 hypothetical protein MMP0903 33, 54, 55
MMP0976 hypothetical protein MMP0976 73, 83
MMP1019 PEGA domain-containing protein 23, 150
MMP1059 hypothetical protein MMP1059 2, 22, 33
MMP1060 cysS cysteinyl-tRNA synthetase 33, 102
MMP1227 cbiE cobalt-precorrin-6Y C(5)-methyltransferase 73, 83
MMP1234 UBA/THIF-type NAD/FAD binding protein 33, 54, 55, 106
MMP1235 moaE molybdopterin biosynthesis MoaE 49, 55, 106, 117, 150
MMP1237 hypothetical protein MMP1237 50, 150
MMP1256 hypothetical protein MMP1256 150, 159
MMP1282 hypothetical protein MMP1282 49, 102, 106, 150
MMP1283 hypothetical protein MMP1283 49, 102, 150
MMP1294 glgA starch synthase 43, 150, 166
MMP1387 hypothetical protein MMP1387 33, 73, 150
MMP1552 3-octaprenyl-4-hydroxybenzoate carboxy-lyase 54, 150
MMP1608 hypothetical protein MMP1608 150, 160
MMP1653 hypothetical protein MMP1653 150, 166
MMP1683 hypothetical protein MMP1683 33, 73
Unanno_13 None 33, 73
Unanno_30 None 37, 73
Unanno_39 None 23, 33
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 MMP1387
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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