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 Network Comparison Type Gene Hugo Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1908 to 1957 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    477 VAV3 Squared vav-3 protein. [swissprot;acc:q9ukw4] 31248.8 37623.4 1.204
    478 BRF1 Ranked transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 228.051 212.321 1.07409
    HIST1H2BL Rooted histone h2b.c (h2b/c). [swissprot;acc:q99880] 50.6084 55.2961 1.09263
    SRP9 Squared signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16318.4 19645.8 1.2039
    STARD13 Measured star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] 9649.61 11053.5 1.14549
    479 EIF5B Squared translation initiation factor if-2. [swissprot;acc:o60841] 24031.6 28929.7 1.20382
    HIST2H2BA Rooted histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 50.6084 55.2961 1.09263
    NOLA1 Ranked nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 228.051 212.321 1.07409
    STARD8 Measured star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] 9649.61 11053.5 1.14549
    480 no value Rooted histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 50.6084 55.2961 1.09263
    CDS1 Squared phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] 26874.6 32347.4 1.20364
    CHRNA2 Measured neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 9649.61 11053.5 1.14549
    NETO2 Ranked neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 237.109 254.667 1.07405
    481 no value Rooted histone h2b. [refseq;acc:nm_175055] 50.6084 55.2961 1.09263
    MAPKAPK3 Measured mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 9649.61 11053.5 1.14549
    NETO1 Ranked neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 237.109 254.667 1.07405
    SRP9 Squared signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16335.9 19660.7 1.20353
    482 no value Rooted histone h2b.s (h2b/s). [swissprot;acc:p57053] 50.6084 55.2961 1.09263
    HNRNPU Ranked heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 237.109 254.667 1.07405
    MAPK14 Measured 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] 9649.61 11053.5 1.14549
    SLC13A3 Squared solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] 26867.3 32335.2 1.20352
    483 no value Rooted histone h2b.d (h2b/d). [swissprot;acc:q99877] 50.6084 55.2961 1.09263
    CHRNA4 Measured neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 9649.61 11053.5 1.14549
    RUNX2 Ranked runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] 237.109 254.667 1.07405
    SLC13A2 Squared solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] 26867.3 32335.2 1.20352
    484 CHRNA3 Measured neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 9649.61 11053.5 1.14549
    HIST3H3 Rooted histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] 50.6084 55.2961 1.09263
    HNRPUL1 Ranked e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 237.109 254.667 1.07405
    SLC13A4 Squared solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] 26867.2 32335 1.20351
    485 HIST1H2BA Rooted testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] 50.6084 55.2961 1.09263
    RPL18 Ranked 60s ribosomal protein l18. [swissprot;acc:q07020] 237.109 254.667 1.07405
    SLC13A1 Squared solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] 26867.2 32335 1.20351
    SPHK2 Measured sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 9649.61 11053.5 1.14549
    486 no value Rooted histone h2b.e (h2b/e). [swissprot;acc:q99879] 50.6084 55.2961 1.09263
    CLEC11A Measured stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] 10908.6 12491.8 1.14513
    MCTS1 Ranked mct-1 protein. [refseq;acc:nm_014060] 226.313 243.03 1.07387
    SCAMP2 Squared secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 26865.9 32332.9 1.20349
    487 no value Rooted tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 50.0015 54.627 1.09251
    MRPL22 Ranked mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] 226.313 243.03 1.07387
    PYCR2 Measured pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] 5277.4 6042.88 1.14505
    SCAMP3 Squared secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] 26865.9 32332.9 1.20349
    488 CLEC3A Measured c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 10872.4 12447 1.14483
    POLR3A Rooted dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 50.4315 46.1703 1.09229
    SART1 Ranked squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] 225.026 209.798 1.07258
    SCAMP1 Squared secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] 26866.1 32333.2 1.20349
    489 CDS2 phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] 26859 32321.2 1.20337
    MRPL12 Rooted 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 50.5505 46.2797 1.09228
    PPM1B Ranked protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 231.276 215.627 1.07257
    PYCR1 Measured pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 5281.11 6044.61 1.14457
    490 ARHGEF7 Ranked rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 220.183 236.015 1.0719

    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/