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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 482 to 531 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    61 Measured PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 4489.19 1.6231 2765.82
    Ranked FOSB protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Low confidence 202.792 1.10831 182.974
    GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] High confidence 266.864 1.25975 336.182
    Squared NDN necdin. [swissprot;acc:q99608] 219048 1.68808 129762
    PSCD3 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Low confidence 92920.4 1.29422 71796.4
    Rooted KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 43.4291 1.36932 31.7159
    SMYD2 set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Low confidence 59.2532 1.11478 66.0541
    62 Measured HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 15464.1 1.13635 17572.7
    PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence 4489.19 1.6231 2765.82
    Ranked FOSL1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Low confidence 202.79 1.10804 183.017
    GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] High confidence 266.865 1.25974 336.181
    Squared MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 219048 1.68808 129762
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Low confidence 92262.9 1.29219 71400.2
    Rooted KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] High confidence 43.4519 1.36847 31.7522
    SMYD1 set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Low confidence 59.2532 1.11478 66.0541
    63 Measured no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 15464.1 1.13635 17572.7
    MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] High confidence 4489.19 1.6231 2765.82
    Ranked no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 266.865 1.25973 336.178
    RBM7 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Low confidence 265.688 1.10749 239.902
    Squared C1GALT1 core1 udp-galactose:n-acetylgalactosamine-alpha-r beta 1,3-galac. [refseq;acc:nm_020156] 73677.6 1.28138 57498.7
    MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] High confidence 219048 1.68808 129762
    Rooted KCNIP2 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 43.4554 1.36835 31.7576
    TBX19 t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Low confidence 61.4851 1.10801 68.1264
    64 Measured HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 15464.1 1.13635 17572.7
    PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] High confidence 4489.19 1.6231 2765.82
    Ranked GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 266.868 1.25965 336.159
    JUND transcription factor jun-d. [swissprot;acc:p17535] Low confidence 202.709 1.10552 183.361
    Squared MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] High confidence 219048 1.68808 129762
    NCDN neurochondrin. [refseq;acc:nm_014284] Low confidence 73677.6 1.28138 57498.7
    Rooted GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 63.8686 1.35128 47.2654
    RAB11FIP4 rab11-family interacting protein 4. [refseq;acc:nm_032932] Low confidence 73.6221 1.10693 81.4944
    65 Measured NEURL neuralized-like. [refseq;acc:nm_004210] High confidence 1657.68 1.6229 2690.25
    SEPT6 septin 6. [swissprot;acc:q14141] Low confidence 13005.8 1.13593 14773.7
    Ranked GNAQ guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] High confidence 267.136 1.25807 336.077
    JUNB transcription factor jun-b. [swissprot;acc:p17275] Low confidence 202.728 1.10546 183.388
    Squared no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] High confidence 219048 1.68808 129762
    SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Low confidence 75490.8 1.26497 95493.3
    Rooted PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 63.8686 1.35128 47.2654
    RAB11FIP3 eferin. [swissprot;acc:o75154] Low confidence 73.6221 1.10693 81.4944
    66 Measured NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] High confidence 1991.03 1.61795 3221.38
    SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Low confidence 4900.7 1.13368 5555.81
    Ranked GNA11 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] High confidence 267.136 1.25807 336.077
    MTUS1 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Low confidence 221.902 1.10518 200.783
    Squared MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] High confidence 219048 1.68808 129762
    SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Low confidence 74803.9 1.26038 94281
    Rooted DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 55.8923 1.10573 61.8016
    PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence 63.8686 1.35128 47.2654
    67 Measured ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 6475.5 1.59177 10307.5
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Low confidence 12176.9 1.1318 13781.8
    Ranked GNAT2 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] High confidence 267.14 1.25805 336.075

    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/