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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type red Interaction Map Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 1558 to 1607 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 753 LBP 224.434 1.04968 235.583
    lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 1569 no value 221.128 1.01646 224.767
    liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 164 SLC39A6 209.299 1.19058 249.187
    loh1cr12. [refseq;acc:nm_058169] 827 LOH12CR1 230.087 1.0431 220.579
    lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] 1810 no value 223.214 1.01171 225.827
    low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 419 FCER2 233.539 1.08417 253.197
    luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 205 LUC7L2 228.1 1.13501 200.968
    luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 206 LUC7L 228.085 1.13472 201.006
    lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] 536 SSB 242.531 1.06778 227.136
    lyl-1 protein (lymphoblastic leukemia derived sequence 1). [swissprot;acc:p12980] 3107 LYL1 0.00001 1 0.00001
    lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] 603 LEF1 225.829 1.0605 212.945
    lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330] 2410 LYPLA1 194.407 1.00362 193.706
    lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260] 2412 LYPLA2P1
    lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] 2116 LIPA 214.632 1.007 213.14
    lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754] 2210 MAN2B1 199.129 1.00645 200.413
    lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698] 2929 LYST 0.00001 1 0.00001
    lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] 1101 KARS 220.291 1.02857 226.584
    m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] 1343 CDC25A 258.558 1.02231 252.916
    m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] 1642 CDC25B 260.269 1.01457 256.531
    m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] 1504 CDC25C 259.439 1.01822 254.797
    mab-21-like protein 1; mab-21-like 1. [refseq;acc:nm_005584] 2786 MAB21L1 0.00001 1 0.00001
    mab-21-like protein 2; mab-21-like 2. [refseq;acc:nm_006439] 2783 MAB21L2
    mad protein (max dimerizer). [swissprot;acc:q05195] 253 MXD1 228 1.11583 204.333
    mago nashi protein homolog. [swissprot;acc:p50606] 2864 MAGOH 0.00001 1 0.00001
    maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 1467 MPP2 228.513 1.01956 232.983
    maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] 2088 MPP3 218.124 1.00781 216.433
    maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] 1479 MPP6 228.469 1.0192 232.855
    major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199] 3013 CENPB 0.00001 1 0.00001
    malate dehydrogenase, cytoplasmic (ec 1.1.1.37). [swissprot;acc:p40925] 3213 MDH1
    malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] 571 MDH2 238.529 1.06528 254.099
    maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 954 GSTZ1 267.447 1.03487 276.773
    malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] 1634 MLYCD 215.772 1.01494 212.596
    mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [refseq;acc:nm_153487] 3070 MDGA1 0.00001 1 0.00001
    mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] 1522 MPI 219.306 1.01766 223.179
    mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] 929 MPDU1 225.955 1.03642 218.015
    mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 2 no value 15 1.86667 28
    map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] 1267 MAPKAPK2 171.231 1.02425 167.177
    map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] 922 MARK1 236.741 1.0372 245.547
    map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] 923 MARK2
    maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 792 no value 224.244 1.04578 234.511
    mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 508 CPA3 177.698 1.07058 190.24
    mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] 2411 PBLD 194.407 1.00362 193.706
    max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 259 RAB24 227.999 1.11562 204.37
    max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 256 MXI1 1.11569 204.357
    max protein. [swissprot;acc:p25912] 425 MAX 227.828 1.082 210.561
    max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 258 MXD4 227.999 1.11564 204.366
    mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] 2331 MIZF 229.258 1.00452 230.294
    mct-1 protein. [refseq;acc:nm_014060] 486 MCTS1 226.313 1.07387 243.03
    megf10 protein. [refseq;acc:nm_032446] 1944 MEGF10 224.341 1.00987 222.148
    megf11 protein. [refseq;acc:nm_032445] 1943 MEGF11 224.34 222.147

    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/