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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2601 to 2650 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    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
    PPP3CB serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] High confidence 218.44 213.44 1.02343
    1308 GRAP2 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Low confidence 199.268 194.914 1.02234
    OCA2 p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] High confidence 218.44 213.439 1.02343
    1309 SFPQ splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Low confidence 200.536 196.157 1.02232
    VBP1 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] High confidence 226.439 221.26 1.02341
    1310 GATAD2A p66 alpha. [refseq;acc:nm_017660] Low confidence 229.478 224.473 1.0223
    PFDN2 prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] High confidence 226.439 221.26 1.02341
    1311 GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Low confidence 229.478 224.473 1.0223
    UXT uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] High confidence 226.439 221.26 1.02341
    1312 no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Low confidence 229.478 224.473 1.0223
    RAD50 rad50 homolog isoform 1. [refseq;acc:nm_005732] High confidence 199.739 204.407 1.02337
    1313 SDCCAG1 serologically defined colon cancer antigen 1. [refseq;acc:nm_004713] Low confidence 202.396 197.985 1.02228
    STAT3 signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] High confidence 222.573 227.75 1.02326
    1314 DNAJB1 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Low confidence 201.948 197.549 1.02227
    STAT4 signal transducer and activator of transcription 4. [swissprot;acc:q14765] High confidence 222.573 227.751 1.02326
    1315 STAT1 signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] 222.574 227.752
    UBQLN4 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] Low confidence 206.697 202.196 1.02226
    1316 SCHIP1 schwannomin interacting protein 1. [refseq;acc:nm_014575] 201.232 196.85
    STAT6 signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] High confidence 222.569 227.739 1.02323
    1317 no value cbf1 interacting corepressor. [refseq;acc:nm_004882] Low confidence 203.649 199.217 1.02225
    CENPJ centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] High confidence 206.773 202.105 1.0231
    1318 GPATCH1 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Low confidence 203.649 199.217 1.02225
    STAT5A signal transducer and activator of transcription 5a. [swissprot;acc:p42229] High confidence 222.546 227.673 1.02304
    1319 ALDH3A2 fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [swissprot;acc:p51648] Low confidence 208.606 213.247 1.02225
    GYS1 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] High confidence 159.75 156.153 1.02304
    1320 MAPK14 mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Low confidence 200.171 195.819 1.02222
    STAT5B signal transducer and activator of transcription 5b. [swissprot;acc:p51692] High confidence 222.544 227.667 1.02302
    1321 C16orf42 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] Low confidence 199.938 195.591 1.02222
    DIMT1L probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] High confidence 226.347 221.259 1.023
    1322 no value endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 159.86 156.275 1.02294
    AGPAT2 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Low confidence 198.322 194.014 1.0222
    1323 NCK2 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] High confidence 205.225 200.625 1.02293
    NGEF neuronal guanine nucleotide exchange factor. [refseq;acc:nm_019850] Low confidence 203.926 199.498 1.0222
    1324 GLB1 beta-galactosidase precursor (ec 3.2.1.23) (lactase) (acid beta- galactosidase). [swissprot;acc:p16278] 203.758 199.335 1.02219
    GYS2 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] High confidence 159.993 156.421 1.02284
    1325 DNAJB4 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] Low confidence 201.909 197.526 1.02219
    WRNIP1 werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] High confidence 217.133 212.289 1.02282

    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/