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 [...,...].
    Gene Rank description Hugo Network Comparison Type red Value Type Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    63 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] MAGEF1 219048 Squared High confidence 129762 1.68808
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] MYO15A 4489.19 Measured 2765.82 1.6231
    putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] RBM7 265.688 Ranked Low confidence 239.902 1.10749
    t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] TBX19 61.4851 Rooted 68.1264 1.10801
    64 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] GBE1 63.8686 High confidence 47.2654 1.35128
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] PYGM 4489.19 Measured 2765.82 1.6231
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] GNG11 266.868 Ranked 336.159 1.25965
    melanoma antigen, family b, 6. [refseq;acc:nm_173523] MAGEB6B 219048 Squared 129762 1.68808
    neurochondrin. [refseq;acc:nm_014284] NCDN 73677.6 Low confidence 57498.7 1.28138
    rab11-family interacting protein 4. [refseq;acc:nm_032932] RAB11FIP4 73.6221 Rooted 81.4944 1.10693
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 15464.1 Measured 17572.7 1.13635
    transcription factor jun-d. [swissprot;acc:p17535] JUND 202.709 Ranked 183.361 1.10552
    65 eferin. [swissprot;acc:o75154] RAB11FIP3 73.6221 Rooted 81.4944 1.10693
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] PYGB 63.8686 High confidence 47.2654 1.35128
    guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] GNAQ 267.136 Ranked 336.077 1.25807
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] no value 219048 Squared 129762 1.68808
    neuralized-like. [refseq;acc:nm_004210] NEURL 1657.68 Measured 2690.25 1.6229
    septin 6. [swissprot;acc:q14141] SEPT6 13005.8 Low confidence 14773.7 1.13593
    septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] SEPT8 75490.8 Squared 95493.3 1.26497
    transcription factor jun-b. [swissprot;acc:p17275] JUNB 202.728 Ranked 183.388 1.10546
    66 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP 55.8923 Rooted 61.8016 1.10573
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL 63.8686 High confidence 47.2654 1.35128
    guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] GNA11 267.136 Ranked 336.077 1.25807
    melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] MAGEA9 219048 Squared 129762 1.68808
    mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] MTUS1 221.902 Ranked Low confidence 200.783 1.10518
    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] NDUFA12 1991.03 Measured High confidence 3221.38 1.61795
    septin 10 isoform 1. [refseq;acc:nm_144710] SEPT10 74803.9 Squared Low confidence 94281 1.26038
    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] SON 4900.7 Measured 5555.81 1.13368
    67 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 6475.5 High confidence 10307.5 1.59177
    brachyury protein (t protein). [swissprot;acc:o15178] T 61.687 Rooted Low confidence 68.2003 1.10559
    guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] GNAT2 267.14 Ranked High confidence 336.075 1.25805
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 12176.9 Measured Low confidence 13781.8 1.1318
    melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] MAGEA8 219048 Squared High confidence 129762 1.68808
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] MYO15A 63.8686 Rooted 47.2654 1.35128
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] UBR4 165.535 Ranked Low confidence 149.799 1.10505
    septin 6. [swissprot;acc:q14141] SEPT6 74378.4 Squared 93531.9 1.25751
    68 60s ribosomal protein l37a. [swissprot;acc:p12751] no value 239.692 Ranked 217.005 1.10455
    beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 6475.5 Measured High confidence 10307.5 1.59177
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] PYGM 63.8686 Rooted 47.2654 1.35128
    guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] GNAZ 267.139 Ranked 336.075 1.25805
    melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 219048 Squared 129762 1.68808
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] UBAC1 19498.1 Measured Low confidence 17265.4 1.12932
    ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2 55.9786 Rooted 61.8641 1.10514
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] UBR4 27909.1 Squared 35068.7 1.25653
    69 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] SLC7A13 6991.78 Measured 7848.45 1.12253
    amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] APBA1 60.7884 Rooted 67.1136 1.10405
    delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] ALDH4A1 80538.1 Squared 64191.7 1.25465
    guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] GNAT1 267.14 Ranked High confidence 336.075 1.25805
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 219048 Squared 129762 1.68808
    neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] NEUROD2 27.9136 Rooted 37.2872 1.33581

    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/