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 Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 408 to 457 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    beta-catenin (pro2286). [swissprot;acc:p35222] 801 CTNNB1 224.445 1.04445 214.894
    beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] 1510 ACTR1B 225.148 1.01795 221.177
    beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] 808 NAPB 212.386 1.04425 221.785
    beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1] 3145 UPB1 0.00001 1 0.00001
    bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] 273 PAPSS1 241.373 1.10763 267.352
    bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 271 no value
    bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 2721 EPRS 221.022 1.00043 221.116
    bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] 740 ATIC 223.58 1.0512 235.027
    bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 1848 BAAT 218.441 1.011 216.064
    biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 1711 HLCS 218.436 1.01337 215.553
    block 23. [sptrembl;acc:q8nhw5] 1091 no value 226.205 1.02941 232.858
    block of proliferation 1. [swissprot;acc:q14137] 512 BOP1 250.794 1.06979 234.433
    blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 1930 no value 196.964 1.01001 198.935
    1932 196.965 198.936
    blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 1928 RHD 196.964 198.935
    bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 1748 no value 215.673 1.01269 212.971
    bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] 793 SERPINB10 224.244 1.04578 234.511
    bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] 3069 BMP5 0.00001 1 0.00001
    bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004] 2896 BMP6
    bone morphogenetic protein 7 precursor (bmp-7) (osteogenic protein 1) (op-1). [swissprot;acc:p18075] 3128 BMP7
    bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 2773 BMP8A
    brachyury protein (t protein). [swissprot;acc:o15178] 2040 T 210.586 1.00854 208.803
    brain protein 16. [refseq;acc:nm_016458] 1847 no value 216.811 1.011 219.195
    brain protein 44. [swissprot;acc:o95563] 742 BRP44 126.215 1.05111 120.078
    branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 2672 BCAT1 210.957 1.00102 210.741
    branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 2687 BCAT2 210.939 1.00087 210.755
    brca1 associated protein. [refseq;acc:nm_006768] 3161 BRAP 0.00001 1 0.00001
    brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 1752 BARD1 216.271 1.01258 218.991
    brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] 294 BCCIP 240.782 1.10356 265.717
    breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 229 BCAR3 226.401 1.12028 202.094
    breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 939 BRCA1 216.501 1.03588 224.27
    breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 691 BCAS2 217.602 1.05532 206.195
    brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] 2713 ARFGEF1 220.521 1.00057 220.395
    brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] 2711 ARFGEF2
    brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 945 ARID1B 212.44 1.03586 205.085
    bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4] 3149 BRPF3 0.00001 1 0.00001
    bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] 2747 BRD7 201.477 1.00018 201.514
    bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696] 3139 BRD1 0.00001 1 0.00001
    bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 2241 BRD2 222.96 1.00618 224.338
    bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 2237 BRD3 222.965 224.343
    bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 2238 BRD4 222.959 224.337
    bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7] 3214 NUB1 0.00001 1 0.00001
    bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] 449 DST 228.463 1.07821 246.33
    bup protein. [refseq;acc:nm_012071] 2911 COMMD3 0.00001 1 0.00001
    bystin. [swissprot;acc:q13895] 1149 BYSL 239.505 1.0271 233.185
    c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] 1766 MTHFD1 228.932 1.01223 231.732
    c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] 2473 MAPK8IP3 218.644 1.003 217.991
    c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 1554 CTBP1 196.215 1.01656 193.018
    c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1558 CTBP2 196.171 1.01655 192.977
    c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 844 CLEC3A 178.033 1.04223 170.82

    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/