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 Hugo Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2564 to 2613 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    1282 CYP4F8 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] High confidence 218.368 213.22 1.02414
    1283 no value casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] Low confidence 205.134 200.628 1.02246
    CYP4X1 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] High confidence 218.368 213.22 1.02414
    1284 CYP4F12 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]
    FAH fumarylacetoacetase (ec 3.7.1.2) (fumarylacetoacetate hydrolase) (beta-diketonase) (faa). [swissprot;acc:p16930] Low confidence 202.294 197.852 1.02245
    1285 CYP4F2 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] High confidence 218.368 213.22 1.02414
    PHB prohibitin. [swissprot;acc:p35232] Low confidence 186.195 182.109 1.02244
    1286 CYP4F11 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] High confidence 218.368 213.22 1.02414
    GNL3 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Low confidence 202.806 198.355 1.02244
    1287 ACSL3 long-chain-fatty-acid--coa ligase 3 (ec 6.2.1.3) (long-chain acyl-coa synthetase 3) (lacs 3). [swissprot;acc:o95573] 201.127 196.714 1.02243
    CYP4A22 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] High confidence 218.368 213.22 1.02414
    1288 C21orf66 gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Low confidence 204.236 199.757 1.02242
    CYP4B1 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] High confidence 218.368 213.22 1.02414
    1289 FLOT1 flotillin-1. [swissprot;acc:o75955]
    GLI2 zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070] Low confidence 203.073 198.619 1.02242
    1290 PPP1R12B protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] 195.789 191.498 1.02241
    SESN1 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] High confidence 218.368 213.22 1.02414
    1291 ACSL4 long-chain-fatty-acid--coa ligase 4 (ec 6.2.1.3) (long-chain acyl-coa synthetase 4) (lacs 4). [swissprot;acc:o60488] Low confidence 201.117 196.709 1.02241
    HAS2 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] High confidence 221.093 226.399 1.024
    1292 CASP7 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] 233.942 228.46
    NONO 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] Low confidence 200.544 196.152 1.02239
    1293 CASP3 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] High confidence 233.942 228.46 1.024
    PSPC1 paraspeckle protein 1. [refseq;acc:nm_018282] Low confidence 200.543 196.152 1.02239
    1294 HAS1 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] High confidence 221.093 226.399 1.024
    SEC31A yeast sec31p homolog. [refseq;acc:nm_014933] Low confidence 204.144 199.676 1.02238
    1295 HAS3 hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] High confidence 221.093 226.399 1.024
    SLC3A1 neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Low confidence 199.695 195.323 1.02238
    1296 SEC31B secretory pathway component sec31b-1. [refseq;acc:nm_015490] 204.174 199.705
    SLC37A1 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] High confidence 209.062 204.174 1.02394
    1297 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] Low confidence 200.193 195.812 1.02237
    PRODH proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] High confidence 209.062 204.174 1.02394
    1298 DLAT dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515] 206.482 211.404 1.02384
    GLI1 zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Low confidence 203.074 198.63 1.02237
    1299 ACO2 aconitate hydratase, mitochondrial precursor (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:q99798] 200.342 195.959
    PMPCB mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] High confidence 217.635 212.575 1.0238
    1300 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Low confidence 199.276 194.918 1.02236
    PMPCA mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] High confidence 217.634 212.576 1.02379
    1301 HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Low confidence 199.276 194.918 1.02236
    TPD52L2 tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] High confidence 206.852 211.757 1.02371
    1302 FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Low confidence 199.276 194.918 1.02236
    UQCRC1 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] High confidence 217.624 212.584 1.02371
    1303 FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Low confidence 199.276 194.918 1.02236
    FHL5 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] High confidence 269.157 275.531 1.02368
    1304 ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Low confidence 199.275 194.918 1.02235
    GSR glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] High confidence 207.387 212.275 1.02357
    1305 GPAM glycerol-3-phosphate acyltransferase, mitochondrial precursor (ec 2.3.1.15) (gpat). [swissprot;acc:q9hcl2] Low confidence 204.064 199.602 1.02235
    PPP3CA serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209] High confidence 218.439 213.436 1.02344
    1306 ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Low confidence 199.275 194.918 1.02235
    PPP3CC serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454] High confidence 218.441 213.441 1.02343
    1307 MTMR1 myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613] Low confidence 204.064 199.602 1.02235

    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/