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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1901 to 1950 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    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
    VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Squared 31248.8 37623.4 1.204
    478 BRF1 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] Ranked 228.051 212.321 1.07409
    HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] Rooted 50.6084 55.2961 1.09263
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Squared 16318.4 19645.8 1.2039
    STARD13 star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Measured 9649.61 11053.5 1.14549
    479 EIF5B translation initiation factor if-2. [swissprot;acc:o60841] Squared 24031.6 28929.7 1.20382
    HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Rooted 50.6084 55.2961 1.09263
    NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Ranked 228.051 212.321 1.07409
    STARD8 star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Measured 9649.61 11053.5 1.14549
    480 no value histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Rooted 50.6084 55.2961 1.09263
    CDS1 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] Squared 26874.6 32347.4 1.20364
    CHRNA2 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Measured 9649.61 11053.5 1.14549
    NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Ranked 237.109 254.667 1.07405
    481 no value histone h2b. [refseq;acc:nm_175055] Rooted 50.6084 55.2961 1.09263
    MAPKAPK3 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Measured 9649.61 11053.5 1.14549
    NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Ranked 237.109 254.667 1.07405
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Squared 16335.9 19660.7 1.20353
    482 no value histone h2b.s (h2b/s). [swissprot;acc:p57053] Rooted 50.6084 55.2961 1.09263
    HNRNPU heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Ranked 237.109 254.667 1.07405
    MAPK14 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] Measured 9649.61 11053.5 1.14549
    SLC13A3 solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] Squared 26867.3 32335.2 1.20352
    483 no value histone h2b.d (h2b/d). [swissprot;acc:q99877] Rooted 50.6084 55.2961 1.09263
    CHRNA4 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Measured 9649.61 11053.5 1.14549
    RUNX2 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] Ranked 237.109 254.667 1.07405
    SLC13A2 solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] Squared 26867.3 32335.2 1.20352
    484 CHRNA3 neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Measured 9649.61 11053.5 1.14549
    HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Rooted 50.6084 55.2961 1.09263
    HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] Ranked 237.109 254.667 1.07405
    SLC13A4 solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] Squared 26867.2 32335 1.20351
    485 HIST1H2BA testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Rooted 50.6084 55.2961 1.09263
    RPL18 60s ribosomal protein l18. [swissprot;acc:q07020] Ranked 237.109 254.667 1.07405
    SLC13A1 solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] Squared 26867.2 32335 1.20351
    SPHK2 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Measured 9649.61 11053.5 1.14549
    486 no value histone h2b.e (h2b/e). [swissprot;acc:q99879] Rooted 50.6084 55.2961 1.09263
    CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Measured 10908.6 12491.8 1.14513
    MCTS1 mct-1 protein. [refseq;acc:nm_014060] Ranked 226.313 243.03 1.07387
    SCAMP2 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Squared 26865.9 32332.9 1.20349
    487 no value tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Rooted 50.0015 54.627 1.09251
    MRPL22 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Ranked 226.313 243.03 1.07387
    PYCR2 pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Measured 5277.4 6042.88 1.14505
    SCAMP3 secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Squared 26865.9 32332.9 1.20349
    488 CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Measured 10872.4 12447 1.14483
    POLR3A dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Rooted 50.4315 46.1703 1.09229

    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/