Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 8714 to 8763 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    1090 no value transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Rooted Subtracted 64.7804 67.9395 3.1591
    ADSSL1 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Divided 67.3406 70.6918 1.04976
    AIPL1 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] Squared Subtracted 22126.7 25398.5 3271.8
    FOXK2 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Measured Divided 5651.07 6164.55 1.09086
    GSK3B glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Subtracted 6439.79 6959.21 519.42
    MYB myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Squared Divided 22799.9 26110 1.14518
    NCALD neurocalcin delta. [swissprot;acc:p29554] Ranked Subtracted 225.104 230.931 5.827
    1091 no value block 23. [sptrembl;acc:q8nhw5] Divided 226.205 232.858 1.02941
    AIP ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Squared Subtracted 22126.7 25398.5 3271.8
    CD109 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Divided 20273.7 23216.9 1.14517
    CLSTN2 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Rooted 82.1701 86.2587 1.04976
    HPCA neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] Ranked Subtracted 225.103 230.928 5.825
    PABPC3 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Measured Divided 5791.05 6316.61 1.09075
    PMM1 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Subtracted 5509.89 6029.29 519.4
    TRUB1 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Rooted 53.3429 50.2017 3.1412
    1092 CLSTN3 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Divided 82.1685 86.2569 1.04976
    FMO1 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Measured Subtracted 5365.14 5884.43 519.29
    HPCAL1 visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235] Ranked 225.094 230.913 5.819
    KIN hskin17 protein. [refseq;acc:nm_012311] Measured Divided 5791.05 6316.61 1.09075
    MYBL1 myb-related protein a (a-myb). [swissprot;acc:p10243] Squared Subtracted 22822.3 26090.1 3267.8
    PIN1 peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] Divided 20273.7 23216.9 1.14517
    POLR3F dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Rooted Subtracted 52.2412 49.113 3.1282
    RPLP0 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] Ranked Divided 226.203 232.855 1.02941
    1093 no value vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Subtracted 218.484 212.675 5.809
    ADSS adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Rooted Divided 67.3413 70.6881 1.0497
    COPA coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Ranked 177.432 182.647 1.02939
    CRAT carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] Measured 5791.05 6316.61 1.09075
    DAZAP1 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Rooted Subtracted 61.5291 64.6568 3.1277
    FMO4 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Measured 5365.22 5884.32 519.1
    IRX4 iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Squared Divided 20273.7 23216.9 1.14517
    RAD54L rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Subtracted 25950.5 29212.5 3262
    1094 ANXA7 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] Ranked Divided 219.655 213.385 1.02938
    API5 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] Subtracted 218.484 212.675 5.809
    LSM1 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Squared 19072.5 22327.5 3255
    MTR 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] Measured 5795.13 6314.19 519.06
    PABPC4 polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] Divided 5791.05 6316.61 1.09075
    PLD1 phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] Squared 25151.8 28800.9 1.14508
    VBP1 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Rooted 58.6583 61.5643 1.04954
    ZMIZ1 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Subtracted 61.529 64.6562 3.1272
    1095 ATXN2L ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Squared Divided 20093.1 23005.6 1.14495
    FTSJ3 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Measured Subtracted 4115.39 4633.96 518.57
    GTPBP3 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Ranked Divided 213.552 207.463 1.02935
    LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Squared Subtracted 18548.7 21798.2 3249.5
    PABPC1 polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] Measured Divided 5791.05 6316.61 1.09075
    PGAM4 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Rooted Subtracted 63.5285 66.6395 3.111
    SEC13 sec13-related protein. [swissprot;acc:p55735] Ranked 218.484 212.675 5.809
    SESN3 sestrin 3. [swissprot;acc:p58005] Rooted Divided 61.5152 64.5624 1.04954
    1096 no value ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Squared 20093.1 23005.6 1.14495
    phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Rooted Subtracted 63.5285 66.6395 3.111
    ATP6V1G3 vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Ranked 218.484 212.675 5.809

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Hugo is the HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/