Organism : Methanococcus maripaludis S2 | Module List :
MMP1236

hypothetical protein MMP1236

CircVis
Functional Annotations (2)
Function System
Uncharacterized conserved protein cog/ cog
thiamine biosynthetic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1236
(Mouseover regulator name to see its description)

MMP1236 is regulated by 13 influences and regulates 0 modules.
Regulators for MMP1236 (13)
Regulator Module Operator
MMP0527
MMP1210
117 combiner
MMP0568 117 tf
MMP1065 117 tf
MMP1065
MMP1210
117 combiner
MMP0097
MMP0527
152 combiner
MMP0460 152 tf
MMP0460 55 tf
MMP0527 55 tf
MMP0907
MMP1023
55 combiner
MMP0907
MMP1646
55 combiner
MMP1023 55 tf
MMP1447 55 tf
MMP0097
MMP1015
22 combiner

Warning: MMP1236 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 10 motifs predicted.

Motif Table (10)
Motif Id e-value Consensus Motif Logo
705 2.10e+01 AAc.CtTGTtaTgactGAAa
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706 6.20e+02 aTaagGttTtt.AAataAtAA
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771 2.40e+01 gcgatgggg.ggAagA.taCctg
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772 1.60e+03 AatTGgTGAa
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889 2.10e+01 TTTcttctagaaTATcccgGgtGA
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890 3.40e+01 TTTTCcagatTttg
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935 9.60e+02 cCgCcgtgAaC
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936 7.30e+03 CcAccaTTGtaaGc
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953 1.80e+00 tgctGGaGgaa
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954 5.30e+02 gAaccacacTccAAA
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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 MMP1236

MMP1236 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Uncharacterized conserved protein cog/ cog
thiamine biosynthetic process go/ biological_process
Module neighborhood information for MMP1236

MMP1236 has total of 103 gene neighbors in modules 22, 55, 117, 142, 152
Gene neighbors (103)
Gene Common Name Description Module membership
Antisense_2 None 1, 22
Antisense_23 None 1, 117
Antisense_5 None 1, 22
MMP0008 DP1 DNA polymerase II small subunit 22, 75, 142
MMP0017 hypothetical protein MMP0017 67, 142
MMP0019 hypothetical protein MMP0019 14, 104, 142
MMP0021 hypothetical protein MMP0021 14, 142
MMP0030 MCM family DNA replication protein 106, 117
MMP0052 putative CBS domain-containing signal transduction protein 13, 117
MMP0071 DNA primase small subunit 72, 152
MMP0085 hypothetical protein MMP0085 22, 106
MMP0113 hypothetical protein MMP0113 23, 75, 142
MMP0119 birA biotin--acetyl-CoA-carboxylase ligase 1, 75, 142
MMP0120 hypothetical protein MMP0120 55, 142
MMP0121 hypothetical protein MMP0121 55, 57
MMP0147 nitrogenase reductase-like protein 17, 22
MMP0177 hypothetical protein MMP0177 83, 117, 152
MMP0225 gldA glycerol dehydrogenase 117, 142
MMP0226 ExsB family transcriptional regulator 13, 117
MMP0231 cysteine-rich small domain 145, 152
MMP0269 hypothetical protein MMP0269 76, 152
MMP0281 ATPase 22, 64
MMP0289 hypD hydrogenase expression/formation protein HypD 12, 117
MMP0304 N-glycosylase/DNA lyase 22, 33, 43, 152
MMP0324 hypothetical protein MMP0324 62, 142
MMP0327 deoA thymidine phosphorylase 94, 152
MMP0439 pyrD dihydroorotate dehydrogenase 1B 117, 119
MMP0453 neutral zinc metallopeptidase 22, 75
MMP0482 hypothetical protein MMP0482 54, 55
MMP0483 hypothetical protein MMP0483 54, 55
MMP0499 hypothetical protein MMP0499 22, 28, 144, 146, 153
MMP0543 hypothetical protein MMP0543 55, 159
MMP0544 MoaA/nifB/pqqE family protein 55, 142
MMP0545 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein 55, 142
MMP0547 RecJ-like protein 22, 166
MMP0570 hypothetical protein MMP0570 22, 65
MMP0585 UspA domain-containing protein 83, 151, 152
MMP0587 napA sodium/hydrogen exchanger 22, 69
MMP0599 cbiJ precorrin-6x reductase CbiJ/CobK 33, 152
MMP0638 hypothetical protein MMP0638 54, 55
MMP0660 apt adenine phosphoribosyltransferase 83, 94, 152
MMP0676 intermediate filament protein 145, 152
MMP0717 hypothetical protein MMP0717 22, 144
MMP0727 uvrB excinuclease ABC subunit B 49, 142
MMP0728 uvrC excinuclease ABC subunit C 90, 142
MMP0760 hypothetical protein MMP0760 22, 67, 92
MMP0761 hypothetical protein MMP0761 22, 64
MMP0788 hypothetical protein MMP0788 58, 117
MMP0792 membrane protein 9, 22
MMP0793 hypothetical protein MMP0793 9, 22
MMP0795 hypothetical protein MMP0795 22, 126
MMP0843 hypothetical protein MMP0843 22, 28
MMP0849 L-lysine/ homoserine-homoserine lactone exporter family protein 95, 117
MMP0871 hypothetical protein MMP0871 22, 153, 166
MMP0902 hypothetical protein MMP0902 12, 49, 55
MMP0903 hypothetical protein MMP0903 33, 54, 55
MMP0986 thyA thymidylate synthase 104, 142
MMP0991 hypothetical protein MMP0991 22, 65
MMP0992 hypothetical protein MMP0992 55, 117
MMP1009 pyrC dihydroorotase 22, 142
MMP1029 hypothetical protein MMP1029 65, 152
MMP1059 hypothetical protein MMP1059 2, 22, 33
MMP1062 hypothetical protein MMP1062 142, 144
MMP1065 BadM/Rrf2 family transcriptional regulator 55, 152
MMP1080 group 1 glycosyl transferase 14, 142
MMP1088 group 1 glycosyl transferase 31, 117
MMP1118 hypothetical protein MMP1118 83, 117
MMP1141 ATP-dependent helicase 75, 142
MMP1228 hypothetical protein MMP1228 4, 22, 142
MMP1233 formate dehydrogenase family accessory protein FdhD 145, 152
MMP1234 UBA/THIF-type NAD/FAD binding protein 33, 54, 55, 106
MMP1235 moaE molybdopterin biosynthesis MoaE 49, 55, 106, 117, 150
MMP1236 hypothetical protein MMP1236 22, 55, 117, 142, 152
MMP1240 Sep-tRNA:Cys-tRNA synthetase 1, 55
MMP1241 hypothetical protein MMP1241 1, 55, 94, 117
MMP1264 hypothetical protein MMP1264 104, 142, 157
MMP1330 hydrogenase assembly chaperone hypC/hupF 100, 117
MMP1346 basic helix-loop-helix dimerization domain-containing protein 49, 67, 142
MMP1372 manB phosphomannomutase 49, 94, 152
MMP1398 dapE diaminopimelate aminotransferase 22, 142
MMP1428 hypothetical protein MMP1428 55, 83
MMP1447 Cro repressor family protein 22, 117
MMP1452 ehaE hypothetical protein MMP1452 22, 117
MMP1453 ehaF hypothetical protein MMP1453 22, 117
MMP1454 ehaG hypothetical protein MMP1454 66, 117, 133
MMP1456 ehaI hypothetical protein MMP1456 66, 117, 133
MMP1459 ehaL hypothetical protein MMP1459 66, 117, 133
MMP1461 ehaN energy conserving hydrogenase A small subunit 117, 133
MMP1477 cbiA cobyrinic acid a,c-diamide synthase 46, 152
MMP1485 moaB molybdenum cofactor biosynthesis protein 104, 142
MMP1487 gapN aldehyde dehydrogenase 55, 152
MMP1549 AP endonuclease 1, 94, 152
MMP1551 ffh signal recognition particle protein Srp54 49, 55, 83
MMP1580 dihydropteroate synthase 22, 145, 152
MMP1597 phosphatidylglycerophosphatase A 22, 142, 144
MMP1607 hypothetical protein MMP1607 49, 55, 83
MMP1619 molybdenum cofactor biosynthesis protein MoeA 117, 152
MMP1636 major facilitator transporter 22, 65, 153
MMP1662 cbiF precorrin-4 C11-methyltransferase 66, 117
MMP1665 HEAT domain-containing protein 66, 117
MMP1679 hypothetical protein MMP1679 117, 151
MMP1686 cbf5 H/ACA RNA-protein complex component Cbf5p 22, 67
Unanno_49 None 95, 117
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 MMP1236
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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