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 4658 to 4707 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    1165 PRODH2 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Measured 6604.44 7183.07 1.08761
    RCAN3 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] Rooted 61.4956 64.4288 1.0477
    TLE3 transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Ranked 219.401 213.785 1.02627
    1166 PSMA5 proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Squared 23379.3 26625.2 1.13884
    RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Rooted 95.094 90.7685 1.04765
    SLC5A8 solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Measured 6606.3 7185.01 1.0876
    TLE2 transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Ranked 219.374 213.759 1.02627
    1167 EN2 homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] 219.399 213.784 1.02626
    NMNAT3 nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Squared 23165.9 26375.7 1.13856
    SLC5A6 sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Measured 6607.68 7186.45 1.08759
    SOCS1 suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] Rooted 62.8958 65.8878 1.04757
    1168 ALDH18A1 delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] Squared 23165.9 26375.7 1.13856
    BUB3 mitotic checkpoint protein bub3. [swissprot;acc:o43684] Measured 5470.44 5949.49 1.08757
    CXXC1 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Ranked 219.399 213.784 1.02626
    GMFG glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] Rooted 62.8958 65.8878 1.04757
    1169 ABT1 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Ranked 219.399 213.784 1.02626
    ASCC2 asc-1 complex subunit p100. [refseq;acc:nm_032204] Rooted 62.8958 65.8878 1.04757
    PDCD11 rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Squared 19625.9 22341.9 1.13839
    ZNF207 zinc finger protein 207. [swissprot;acc:o43670] Measured 5470.44 5949.49 1.08757
    1170 no value cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Ranked 219.399 213.784 1.02626
    FKBP1A fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] Rooted 62.8958 65.8878 1.04757
    LBP lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Squared 20923.6 23813.2 1.1381
    SUMO3 ubiquitin-like protein smt3a. [swissprot;acc:p55854] Measured 5826.34 6335.98 1.08747
    1171 no value 40s ribosomal protein s28. [swissprot;acc:p25112] Rooted 70.4215 73.7627 1.04745
    ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Measured 5826.29 6335.93 1.08747
    HECW1 hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Ranked 219.399 213.784 1.02626
    SPCS2 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Squared 20923.6 23813.2 1.1381
    1172 no value transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Ranked 219.375 213.767 1.02623
    ACRC acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Measured 5826.32 6335.95 1.08747
    MAP3K7 mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Rooted 63.4397 66.4483 1.04742
    UMPS uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Squared 20923.6 23813.2 1.1381
    1173 CABC1 chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] Measured 5799.35 6305.95 1.08735
    CLPTM1 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] Squared 20923.6 23813.2 1.1381
    DPH1 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] Ranked 229.243 235.246 1.02619
    OXA1L cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Rooted 60.9172 63.8009 1.04734
    1174 BPI bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Squared 20923.6 23813.2 1.1381
    COPE coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] Ranked 187.964 192.849 1.02599
    MRPL34 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] Rooted 60.9172 63.8009 1.04734
    TATDN1 cda11 protein. [refseq;acc:nm_032026] Measured 5874.11 6387.23 1.08735
    1175 ADCK2 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] 5799.35 6305.95
    ATP6V0C vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Ranked 218.186 212.672 1.02593
    PLTP phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Squared 20923.6 23813.2 1.1381
    PRSS12 neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Rooted 61.2655 64.1634 1.0473
    1176 ADCK4 aarf domain containing kinase 4. [refseq;acc:nm_024876] Measured 5799.35 6305.95 1.08735
    RNF44 ring finger protein 44. [refseq;acc:nm_014901] Rooted 61.2655 64.1634 1.0473
    SGCZ sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Ranked 218.186 212.672 1.02593
    SLC35B1 solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Squared 22201.6 25263.1 1.1379
    1177 ACBD3 golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] Ranked 218.186 212.672 1.02593
    ADCK1 aarf domain containing kinase 1. [refseq;acc:nm_020421] Measured 5799.35 6305.95 1.08735
    MPI mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Squared 22813.2 25958.3 1.13786

    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/