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 green Interaction Map Network Comparison Type Filtered red network_comparison
    Results: HTML CSV LaTeX Showing element 201 to 250 of 3228 in total
    Value Type  : Measured
    Interaction Map  : High confidence
    Network Comparison Type  : Divided
    Filtered  : 1
    description
    		Rank
    		green
    		red
    		network_comparison
    adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] 2444 6695.67 6478.14 1.03358
    adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] 2441 6695.58 6477.82 1.03362
    adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979] 2870 0.00001 0.00001 1
    adaptor-associated kinase 1. [refseq;acc:nm_014911] 2282 6048.91 5783.73 1.04585
    adaptor-related protein complex 1, mu 1 subunit (mu-adaptin 1) (adaptor protein complex ap-1 mu-1 subunit) (golgi adaptor ha1/ap1 adaptin mu-1 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 1) (clathrin coat assembly protein ap47) (clathrin coat associated protein ap47) (ap-mu chain family member mu1a). [swissprot;acc:q9bxs5] 2007 6018.72 5684.61 1.05877
    adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] 2010 6003.67 5671.62 1.05855
    adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 2519 6113.96 5964.17 1.02511
    adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263] 1581 6833.59 6376.12 1.07175
    adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 940 6113.35 5568.96 1.09775
    adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326] 1851 6549.03 6156.28 1.0638
    adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 401 4479.76 5201.41 1.16109
    adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 400
    adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 2385 3569.68 3716.43 1.04111
    adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 2228 3484.97 3650.82 1.04759
    adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] 1640 7964 7444.28 1.06981
    adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 679 7282.94 6503.1 1.11992
    adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] 680 7282.5 6503.03 1.11986
    adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] 1541 6427.17 5989.3 1.07311
    adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 1562 6419.11 5984.88 1.07255
    adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] 1884 6195.48 5826 1.06342
    adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] 2723 5583.64 5603.24 1.00351
    adiponectin receptor 2. [refseq;acc:nm_024551] 317 3762.56 3153.1 1.19329
    adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] 1119 5798.38 5322.16 1.08948
    adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] 1118
    adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 1117
    adp-ribosylation factor 1. [swissprot;acc:p32889] 1824 5997 5633.44 1.06454
    adp-ribosylation factor 3. [swissprot;acc:p16587] 1826
    adp-ribosylation factor 4. [swissprot;acc:p18085] 1819
    adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] 982 7296.51 6654.42 1.09649
    adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 1830 5997 5633.44 1.06454
    adp-ribosylation factor-like protein 1. [swissprot;acc:p40616] 1619 6464.5 6035.6 1.07106
    adp-ribosylation factor-like protein 3. [swissprot;acc:p36405] 1534 6350.53 5916.05 1.07344
    adp-ribosylation factor-like protein 4. [swissprot;acc:p40617] 883 6517.69 5912.84 1.10229
    adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 881
    adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 548 9405.85 8268.19 1.13759
    af-6 protein. [swissprot;acc:p55196] 2076 6067.27 5746.65 1.05579
    afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] 1543 5865.33 5466 1.07306
    aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] 1141 6303.93 5790.65 1.08864
    aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] 1131 6303.92
    ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] 1904 5530.11 5204.25 1.06261
    alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 2415 7223.09 6956.62 1.0383
    alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] 2414 7223.14 6956.32 1.03836
    alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] 2599 4438.77 4367.69 1.01627
    alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 2249 7153.66 6834.03 1.04677
    aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353] 3222 0.00001 0.00001 1
    aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 2992
    aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278] 2960
    alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 1369 6241.16 5786.71 1.07853
    alpha crystallin a chain. [swissprot;acc:p02489] 2875 0.00001 0.00001 1
    alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] 3082

    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/