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 [...,...].
    description Rank Value Type Gene Interaction Map green Network Comparison Type Filtered red network_comparison
    Results: HTML CSV LaTeX Showing element 1400 to 1449 of 3228 in total
    Value Type  : Measured
    Interaction Map  : High confidence
    Network Comparison Type  : Divided
    Filtered  : 1
    description
    		Rank
    		green
    		red
    		network_comparison
    indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] 1676 6193.02 5791.14 1.0694
    inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] 2714 5583.64 5603.24 1.00351
    inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 2739 4890.64 4877.74 1.00264
    inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] 2736 4902.08 4887.59 1.00296
    inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] 1901 5530.11 5204.25 1.06261
    inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] 1902
    inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] 2245 6049.61 5776.96 1.0472
    inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 2243
    inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] 1981 5800.97 5475.74 1.05939
    inositol polyphosphate multikinase. [refseq;acc:nm_152230] 1542 5865.33 5466 1.07306
    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] 559 7007.7 6167.93 1.13615
    inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] 557
    inositol polyphosphate-5-phosphatase; phosphatidylinositol polyphosphate 5-phosphatase type iv; phosphatidylinositol (4,5) bisphosphate 5-phosphatase. [refseq;acc:nm_019892] 2912 0.00001 0.00001 1
    inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] 1717 6484.94 6069.65 1.06842
    inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] 1716 6485.85 6070.41 1.06844
    insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663] 2626 7534.05 7424.26 1.01479
    insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] 2638 7525.14 7433.72 1.0123
    integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] 986 6976.1 6362.64 1.09642
    integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] 984
    integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] 985
    integral membrane protein cii-3b. [sptrembl;acc:o75609] 2511 6415.04 6256.42 1.02535
    integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006] 3224 0.00001 0.00001 1
    integrin alpha-6 precursor (vla-6) (cd49f). [swissprot;acc:p23229] 3158
    integrin alpha-7 precursor. [swissprot;acc:q13683] 2978
    integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [swissprot;acc:p05556] 2905
    integrin beta-2 precursor (cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta-subunit) (cd18) (complement receptor c3 beta- subunit). [swissprot;acc:p05107] 2873
    integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] 3195
    integrin beta-7 precursor. [swissprot;acc:p26010] 2951
    integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] 1869 6463.12 6076.66 1.0636
    interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894] 1787 5744.78 5386.48 1.06652
    interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [refseq;acc:nm_004515] 2930 0.00001 0.00001 1
    interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 1090 6164.55 5651.07 1.09086
    interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 583 7644.62 6739.81 1.13425
    interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] 994 6355.71 5800.95 1.09563
    intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] 2558 5187.78 5291.65 1.02002
    intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] 2560
    iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] 2668 8169.38 8222.61 1.00652
    iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] 1447 5510.45 5117.85 1.07671
    ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 1738 6282.97 5885.08 1.06761
    isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] 1122 8646.38 7937.72 1.08928
    isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p50213] 1417 5775.24 5360.39 1.07739
    isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:o43837] 1418
    isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553] 1419
    isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 1330 6244.56 5779.83 1.08041
    itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] 1605 6617.91 6176.82 1.07141
    j domain containing protein 1. [swissprot;acc:q9ukb3] 1971 4126.96 4374.32 1.05994
    j domain protein c21orf55. [swissprot;acc:q9nx36] 2708 9012.42 8979.78 1.00363
    j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 693 8647.74 7725.1 1.11943
    jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0] 2775 0.00001 0.00001 1
    jm1 protein. [refseq;acc:nm_014008] 810 6427.79 5794.8 1.10923

    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
    - 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/