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 Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		red
    		green
    		network_comparison
    carboxypeptidase b precursor. [refseq;acc:nm_020361] 509 177.698 190.239 1.07057
    carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 717 223.121 211.685 1.05402
    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] 715
    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] 1698 217.624 214.69 1.01367
    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] 226 239.991 269.238 1.12187
    casein kinase i alpha s-like. [refseq;acc:nm_145203] 1495 229.459 225.237 1.01874
    casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] 1496
    casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] 1721 227.125 224.164 1.01321
    casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 1710 227.225 224.21 1.01345
    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] 936 232.473 224.372 1.03611
    casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 863 240.194 230.957 1.03999
    casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 864
    caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] 1292 233.942 228.46 1.024
    catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 1834 180.409 182.459 1.01136
    cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 1667 214.898 211.898 1.01416
    cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] 1426 214.717 219.157 1.02068
    cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] 1425
    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] 572 227.86 213.945 1.06504
    cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 762 213.256 203.237 1.0493
    ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 556 207.27 194.368 1.06638
    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] 36 260.532 204.309 1.27519
    ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 408 255.112 234.804 1.08649
    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] 1390 218.47 213.875 1.02148
    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] 2075 221.703 223.483 1.00803
    cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 418 233.539 253.197 1.08417
    cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 420
    cda11 protein. [refseq;acc:nm_032026] 1579 213.181 209.732 1.01644
    cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] 1778 216.878 214.286 1.0121
    cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 437 209.921 226.459 1.07878
    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] 692 217.602 206.195 1.05532
    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] 2155 200.063 198.71 1.00681
    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] 2739 198.278 198.321 1.00022
    cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 1585 168.145 170.888 1.01631
    cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 1481 208.432 204.516 1.01915
    cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 1583 168.091 170.837 1.01634
    cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 1581 168.002 170.753 1.01637
    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/