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 Gene Rank Value Type Network Comparison Type Filtered Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 3228 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Filtered  : 1
    Interaction Map  : High confidence
    description
    		Rank
    		red
    		green
    		network_comparison
    carboxypeptidase b precursor. [refseq;acc:nm_020361] 239 7711.38 6265.8 1.23071
    carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 719 6593.17 7364.55 1.117
    carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] 717
    carcinoma related gene. [refseq;acc:nm_016041] 3179 0.00001 0.00001 1
    carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] 1093 5791.05 6316.61 1.09075
    carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786] 2885 0.00001 0.00001 1
    cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 2220 3936.2 3755.33 1.04816
    casein kinase i alpha s-like. [refseq;acc:nm_145203] 953 4906.33 5382.5 1.09705
    casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] 954
    casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] 1035 5054.73 5530.23 1.09407
    casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 1030 5048.33 5523.85 1.09419
    casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0] 2830 0.00001 0.00001 1
    casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368] 2986
    casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4] 2901
    casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] 1245 4835.55 5243.23 1.08431
    casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 851 4307.12 4755.03 1.10399
    casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 852
    caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] 948 4633.48 5084.24 1.09728
    catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 616 11222.2 9948.93 1.12798
    cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 914 6513.45 7161 1.09942
    cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] 2238 5902.27 6181.21 1.04726
    cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] 2237 5902.26
    caveolin-1. [swissprot;acc:q03135] 3099 0.00001 0.00001 1
    caveolin-3 (m-caveolin). [swissprot;acc:p56539] 2779
    cbf1 interacting corepressor. [refseq;acc:nm_004882] 1651 5944.24 6358.1 1.06962
    cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 507 6875.08 7858.38 1.14302
    ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 257 6417.31 7858.12 1.22452
    ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 137 3620.77 4763.34 1.31556
    ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 369 3583.56 4194.95 1.17061
    ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [refseq;acc:nm_014516] 3163 0.00001 0.00001 1
    ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] 2289 5783.76 6048.94 1.04585
    ccr4-not transcription complex, subunit 6-like. [refseq;acc:nm_144571] 2958 0.00001 0.00001 1
    ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 3226
    ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [swissprot;acc:q9uff9] 2890
    cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] 1445 5117.85 5510.45 1.07671
    cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 2753 4521.42 4521.87 1.0001
    cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 2755
    cda11 protein. [refseq;acc:nm_032026] 1174 5874.11 6387.23 1.08735
    cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] 1995 6174.74 6538.73 1.05895
    cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 1611 5497.73 5132.35 1.07119
    cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] 419 5493.1 6350.19 1.15603
    cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [swissprot;acc:p51948] 3209 0.00001 0.00001 1
    cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] 981 6654.42 7296.51 1.09649
    cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] 1660 7433.73 7950.61 1.06953
    cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 363 12780.7 10876.4 1.17509
    cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 2387 8265.85 7940.87 1.04092
    cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 361 12787.6 10880.5 1.17528
    cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 359 12798.9 10887.2 1.17559
    cell division protein kinase 5 (ec 2.7.1.-) (tau protein kinase ii catalytic subunit) (tpkii catalytic subunit) (serine/threonine protein kinase pssalre). [swissprot;acc:q00535] 2850 0.00001 0.00001 1
    cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] 2990

    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
    - 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/