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 network_comparison green
    Results: HTML CSV LaTeX Showing element 3025 to 3074 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    190 no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Squared Divided Low confidence 51507.8 1.10898 46446.1
    AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] High confidence 71389.9 1.34525 96037.6
    DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Measured 4571.89 1.28281 5864.86
    FLAD1 fad synthetase. [refseq;acc:nm_025207] Ranked Subtracted 241.373 25.979 267.352
    FMO5 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Divided Low confidence 210.557 1.0524 200.074
    Rooted 69.0062 1.06159 73.256
    GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] High confidence 149.165 1.15009 129.699
    GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked Subtracted Low confidence 211.383 10.593 221.976
    LIPF triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Squared 54309.4 5117 49192.4
    MAPK11 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] High confidence 42411.6 13390.5 55802.1
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted Low confidence 71.1262 4.3214 75.4476
    PHF12 phd finger protein 12; phd zinc finger transcription factor. [refseq;acc:nm_020889] Measured 10745.7 585.7 10160
    RAP1GAP rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Rooted High confidence 47.6504 10.72 36.9304
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Measured 4366.44 1533.32 5899.76
    Ranked Divided 226.582 1.14179 198.444
    TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Measured Low confidence 6480.93 1.07485 6966.05
    191 no value bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Ranked Subtracted High confidence 241.373 25.979 267.352
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Measured 4366.44 1533.32 5899.76
    Ranked Divided 226.582 1.14179 198.444
    AGBL3 similar to atp/gtp-binding protein. [sptrembl;acc:q8nem8] Measured Low confidence 9385.4 1.07469 10086.4
    AQP5 aquaporin 5. [swissprot;acc:p55064] Squared High confidence 71388.5 1.34525 96035.2
    ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Rooted Subtracted 116.797 10.686 106.111
    CDC14C cdc14 homolog b isoform 2. [refseq;acc:nm_033331] Squared Low confidence 53433.9 5101.1 48332.8
    CYBB cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] Rooted Divided 69.9165 1.06154 74.2189
    ICK intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Squared 45402.8 1.10897 50350.5
    PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Rooted High confidence 63.1192 1.14995 72.584
    PXK px serine/threonine kinase. [refseq;acc:nm_017771] Ranked Subtracted Low confidence 196.372 10.575 206.947
    RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] Measured 10730.1 581.9 10148.2
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Divided High confidence 4638.1 1.27712 5923.4
    SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Ranked Low confidence 201.43 1.05224 191.43
    SPHK1 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Squared Subtracted High confidence 42411.6 13390.5 55802.1
    TPM4 tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Rooted Low confidence 70.8512 4.3197 75.1709
    192 no value bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] Ranked 196.372 10.575 206.947
    small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Measured High confidence 10807.4 1531.1 12338.5
    AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Squared Divided 71387.4 1.34524 96033.4
    ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Measured 17757.5 1.26767 14008
    CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Subtracted Low confidence 5674.92 580.26 6255.18
    DPAGT1 udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Squared High confidence 42411.6 13390.5 55802.1
    DUOX2 dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] Rooted Low confidence 69.8853 4.3157 74.201
    KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Squared 51551.5 5094.4 46457.1
    LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Ranked High confidence 241.373 25.979 267.352
    MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Divided 227.491 1.14055 199.458
    NOX5 nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Rooted Low confidence 69.9161 1.06154 74.2187
    RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted High confidence 116.792 10.685 106.107
    RC3H2 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Ranked Divided Low confidence 217.341 1.05214 206.571
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Rooted High confidence 53.6107 1.14877 61.5862
    SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Squared Low confidence 51506.6 1.10896 46445.8
    TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Measured 9385.4 1.07469 10086.4
    193 no value cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Subtracted 5752.65 577.38 6330.03
    DLC1 rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Squared High confidence 42411.6 13390.5 55802.1

    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/