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 Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2430 to 2479 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		red
    		green
    		network_comparison
    1215 PPIE Subtracted peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] 174.387 179.697 5.31
    1216 COPZ2 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
    ZMIZ1 Divided retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] 218.269 212.918 1.02513
    1217 HAS2 Subtracted hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] 221.093 226.399 5.306
    QRSL1 Divided glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 211.959 217.258 1.025
    1218 FAAH fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519]
    HAS1 Subtracted hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] 221.093 226.399 5.306
    1219 COTL1 Divided coactosin-like protein. [swissprot;acc:q14019] 211.959 217.258 1.025
    HAS3 Subtracted hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] 221.093 226.399 5.306
    1220 QRSL1 glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 211.959 217.258 5.299
    UNG Divided uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] 1.025
    1221 FAAH Subtracted fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] 5.299
    PET112L Divided probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] 1.025
    1222 COTL1 Subtracted coactosin-like protein. [swissprot;acc:q14019] 5.299
    TPD52L1 Divided tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] 206.774 211.936 1.02496
    1223 TPD52 tumor protein d52 (n8 protein). [swissprot;acc:p55327] 206.771 211.926 1.02493
    UNG Subtracted uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] 211.959 217.258 5.299
    1224 FPGS Divided folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 225.906 231.524 1.02487
    PET112L Subtracted probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] 211.959 217.258 5.299
    1225 IL4I1 interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] 219.55 214.288 5.262
    UBE2E1 Divided ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] 166.846 170.989 1.02483
    1226 FDX1 Subtracted adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 191.139 185.882 5.257
    UBE2E4P Divided ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] 166.846 170.989 1.02483
    1227 GCLM Subtracted glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] 213.079 218.325 5.246
    PYCR2 Divided pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] 172.365 168.219 1.02465
    1228 GCLC Subtracted glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506] 213.079 218.325 5.246
    GCLM Divided glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] 1.02462
    1229 no value Subtracted integral membrane protein cii-3b. [sptrembl;acc:o75609] 207.646 212.891 5.245
    GCLC Divided glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506] 213.079 218.325 1.02462
    1230 IL4I1 interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] 219.55 214.288 1.02456
    SDHC Subtracted succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] 207.644 212.888 5.244
    1231 PGAM4 Divided putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 212.724 207.637 1.0245
    SDHB Subtracted succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] 207.931 213.175 5.244
    1232 no value alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 209.649 204.406 5.243
    PYCR1 Divided pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 172.543 168.417 1.0245
    1233 no value 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] 212.724 207.637
    SEPT1 Subtracted septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 142.077 136.846 5.231
    1234 PGAM2 Divided phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259] 212.724 207.637 1.0245
    UBB Subtracted ubiquitin. [swissprot;acc:p02248] 209.6 204.372 5.228
    1235 no value Divided keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 219.356 224.723 1.02447
    COPA Subtracted coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] 177.432 182.647 5.215
    1236 no value Divided keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 219.354 224.699 1.02437
    VBP1 Subtracted prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 226.439 221.26 5.179
    1237 no value Divided keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] 219.354 224.699 1.02437
    PFDN2 Subtracted prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] 226.439 221.26 5.179
    1238 no value Divided keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 219.354 224.699 1.02437
    UXT Subtracted uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] 226.439 221.26 5.179
    1239 no value Divided keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] 219.354 224.699 1.02437
    STAT4 Subtracted signal transducer and activator of transcription 4. [swissprot;acc:q14765] 222.573 227.751 5.178
    1240 no value Divided keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 219.354 224.7 1.02437

    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/