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 63324 to 63373 of 66312 in total
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		red
    		green
    		network_comparison
    4688 MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Ranked Divided 178.882 179.908 1.00574
    PIP5K1C phosphatidylinositol-4-phosphate 5-kinase, type i, gamma; phosphatidylinositol-4-phosphate 5-kinase i-gamma; diphosphoinositide kinase; type i pip kinase; ptdins(4)p-5-kinase. [refseq;acc:nm_012398] Squared 50469.9 49691.4 1.01567
    PPP1R14A protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Subtracted 28662.5 27991 671.5
    RALBP1 rala binding protein 1; rala-binding protein. [refseq;acc:nm_006788] Ranked 206.188 205.032 1.156
    SEMA6D semaphorin 6d isoform 3 precursor. [refseq;acc:nm_153617] Measured 8490.93 8607.91 116.98
    4689 no value melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Ranked Divided 178.882 179.908 1.00574
    ABCD1 adrenoleukodystrophy protein (aldp). [swissprot;acc:p33897] Measured 7487.95 7599.18 1.01485
    ELOVL5 homolog of yeast long chain polyunsaturated fatty acid elongatio; homolog of yeast long chain polyunsaturated fatty acid elongation enzyme 2. [refseq;acc:nm_021814] Rooted 70.3775 71.6688 1.01835
    IKZF5 zinc finger protein, subfamily 1a, 5; zinc finger transcription factor pegasus. [refseq;acc:nm_022466] Measured Subtracted 8490.93 8607.91 116.98
    LRRN1 leucine rich repeat neuronal 1. [refseq;acc:nm_020873] Ranked 206.041 204.886 1.155
    MFAP4 microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Squared 28662.5 27991 671.5
    PIP5K1A phosphatidylinositol-4-phosphate 5-kinase, type i, alpha. [refseq;acc:nm_003557] Divided 50469.9 49691.4 1.01567
    YIF1A yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Rooted Subtracted 71.3973 72.7639 1.3666
    4690 no value elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9] Divided 70.3775 71.6674 1.01833
    ADSS adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared 48918.1 49683.5 1.01565
    AGXT2L1 alanine-glyoxylate aminotransferase 2-like 1. [refseq;acc:nm_031279] Measured 8641.8 8769.61 1.01479
    LRRN3 leucine rich repeat neuronal 3; leucine-rich repeat protein, neuronal 3. [refseq;acc:nm_018334] Ranked Subtracted 206.041 204.886 1.155
    MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Divided 178.882 179.908 1.00574
    MRPL2 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Rooted Subtracted 69.8609 71.2265 1.3656
    PAFAH1B1 platelet-activating factor acetylhydrolase ib alpha subunit (ec 3.1.1.47) (paf acetylhydrolase 45 kda subunit) (paf-ah 45 kda subunit) (paf-ah alpha) (pafah alpha) (lissencephaly-1 protein) (lis- 1). [swissprot;acc:p43034] Measured 8490.93 8607.91 116.98
    PPP1R14D protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Squared 28662.5 27991 671.5
    4691 ANAPC2 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] Rooted Divided 70.7178 72.0088 1.01826
    FCN2 ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Squared Subtracted 28662.5 27991 671.5
    HTATIP2 hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] Rooted 75.6274 76.9908 1.3634
    MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Ranked Divided 178.882 179.908 1.00574
    PCSK7 proprotein convertase subtilisin/kexin type 7 precursor (ec 3.4.21.-) (proprotein convertase pc7) (subtilisin/kexin-like protease pc7) (prohormone convertase pc7) (pc8) (hpc8) (lymphoma proprotein convertase). [swissprot;acc:q16549] Measured Subtracted 8618.71 8735.6 116.89
    PI4K2A phosphatidylinositol 4-kinase type ii. [refseq;acc:nm_018425] Squared Divided 45731.7 45027.8 1.01563
    POLR2J dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Measured 7821.27 7936.9 1.01478
    THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Ranked Subtracted 213.765 214.908 1.143
    4692 no value dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Measured Divided 7821.63 7936.58 1.0147
    hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Ranked 178.882 179.908 1.00574
    protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Squared Subtracted 28662.5 27991 671.5
    BNIP1 bcl2/adenovirus e1b 19-kda protein-interacting protein 1. [swissprot;acc:q12981] Rooted Divided 70.9575 72.2531 1.01826
    COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Ranked Subtracted 213.766 214.907 1.141
    GNB4 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Rooted 71.1925 72.5547 1.3622
    IDE insulin-degrading enzyme (ec 3.4.24.56) (insulysin) (insulinase) (insulin protease). [swissprot;acc:p14735] Measured 8618.71 8735.6 116.89
    ME2 nad-dependent malic enzyme, mitochondrial precursor (ec 1.1.1.38) (nad-me) (malic enzyme 2). [swissprot;acc:p23368] Squared Divided 46416.5 45703.4 1.0156
    4693 no value dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Measured 7821.58 7936.56 1.0147
    germ cell-less. [refseq;acc:nm_022471] Rooted Subtracted 69.4434 70.8052 1.3618
    CCNK cyclin k. [swissprot;acc:o75909] Divided 70.9575 72.2531 1.01826
    FXN frataxin, mitochondrial precursor (friedreich's ataxia protein) (fxn). [swissprot;acc:q16595] Squared Subtracted 50203.9 50875.1 671.2
    HSD11B1 corticosteroid 11-beta-dehydrogenase, isozyme 1 (ec 1.1.1.146) (11-dh) (11-beta-hydroxysteroid dehydrogenase 1) (11-beta-hsd1). [swissprot;acc:p28845] Measured 7487.12 7603.84 116.72
    MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked Divided 178.882 179.908 1.00574
    PI4K2B phosphatidylinositol 4-kinase type-ii beta; likely ortholog of mouse phosphatidylinositol 4-kinase type 2 beta. [refseq;acc:nm_018323] Squared 45731.4 45029.2 1.01559
    TSPAN31 sarcoma amplified sequence. [swissprot;acc:q12999] Ranked Subtracted 201.93 200.79 1.14
    4694 no value 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Rooted 69.3287 70.6863 1.3576
    ATP7B copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] Squared Divided 49977.2 50754.4 1.01555
    LAMB1 laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942] Ranked Subtracted 204.169 203.033 1.136
    NDN necdin. [swissprot;acc:q99608] Divided 178.882 179.908 1.00574
    OXR1 oxidation resistance 1. [refseq;acc:nm_181354] Measured 8287.83 8409.57 1.01469

    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/