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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1858 to 1907 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    465 CHRNA7 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Ranked 248.152 267.226 1.07686
    E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Measured 3847.31 4409.22 1.14605
    TRIT1 trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Squared 25310.2 30537 1.20651
    466 ADCY6 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Ranked 248.152 267.226 1.07686
    ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Squared 25513.6 30779.5 1.2064
    E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Measured 3847.31 4409.22 1.14605
    VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Rooted 66.089 72.3555 1.09482
    467 ADCY5 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Ranked 248.152 267.226 1.07686
    MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] Measured 4864.25 5573.62 1.14583
    NUCB1 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Squared 23531.7 28371.6 1.20568
    RPS5 40s ribosomal protein s5. [swissprot;acc:p46782] Rooted 50.4649 46.1093 1.09446
    468 CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 107.178 117.276 1.09422
    LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Ranked 248.152 267.226 1.07686
    MLH1 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Squared 23531.7 28371.6 1.20568
    RBBP4 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Measured 4869.15 5578.02 1.14558
    469 no value 60s ribosomal protein l9. [swissprot;acc:p32969] Rooted 51.1334 46.7335 1.09415
    FEM1B fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Ranked 248.152 267.226 1.07686
    NOL1 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Measured 3831.17 4388.74 1.14554
    NUCB2 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Squared 23531.7 28371.6 1.20568
    470 BOP1 block of proliferation 1. [swissprot;acc:q14137] Measured 3796.24 4348.59 1.1455
    LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Ranked 248.152 267.226 1.07686
    PPP2R1B serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Squared 10418.3 8641.84 1.20557
    SNW1 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Rooted 60.0148 65.6429 1.09378
    471 LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Ranked 248.152 267.226 1.07686
    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] Measured 9649.61 11053.5 1.14549
    PGK2 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Squared 28188.7 33982.7 1.20554
    VAV2 vav-2 protein. [swissprot;acc:p52735] Rooted 66.088 72.2597 1.09339
    472 ENO2 gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Squared 28190.4 33984.1 1.20552
    PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Rooted 50.3767 46.0753 1.09336
    SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Ranked 248.152 267.226 1.07686
    SPHK1 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Measured 9649.61 11053.5 1.14549
    473 DPAGT1 udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]
    ENO3 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Squared 28190.4 33984.1 1.20552
    PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Ranked 225.661 209.651 1.07637
    SEPHS2 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Rooted 62.574 68.4128 1.09331
    474 DLC1 rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Measured 9649.61 11053.5 1.14549
    ENO1 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Squared 28190.4 33984.1 1.20552
    KCNA2 potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Ranked 226.789 210.818 1.07576
    MICAL2 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Rooted 62.574 68.4128 1.09331
    475 INPP4B inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866]
    KCNA1 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Ranked 226.727 210.816 1.07547
    MAPKAPK2 map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Measured 9649.61 11053.5 1.14549
    PGK1 phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Squared 28192 33985.3 1.20549
    476 CHRNA6 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Measured 9649.61 11053.5 1.14549
    KCNA4 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Ranked 226.681 210.814 1.07527
    SEPHS1 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Rooted 62.574 68.4128 1.09331
    VAV1 vav proto-oncogene. [swissprot;acc:p15498] Squared 31223.8 37614.3 1.20467
    477 INPP4A inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Rooted 62.574 68.4128 1.09331
    ISCU nitrogen fixation cluster-like. [refseq;acc:nm_014301] Measured 9649.61 11053.5 1.14549
    NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Ranked 251.926 234.547 1.0741

    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/