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 red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 391 to 440 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] 1567 BBS7 221.128 224.767 1.01646
    barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531] 2804 BANF1 0.00001 0.00001 1
    basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 933 BHLHB5 159.165 164.951 1.03635
    basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 2715 no value 216.018 215.903 1.00053
    bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061] 2950 TEGT 0.00001 0.00001 1
    bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745] 2776 BCOR
    beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] 1636 BECN1 202.358 199.408 1.01479
    bet3 homolog. [swissprot;acc:o43617] 567 TRAPPC3 129.219 121.261 1.06563
    beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 1945 ADD2 224.343 222.151 1.00987
    beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] 2361 ENO3 207.186 208.046 1.00415
    beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 301 ALG1 150.982 166.372 1.10193
    beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] 2576 SNTB1 213.422 213.75 1.00154
    beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] 2578 SNTB2
    beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 50 ARRB1 133 105 1.26667
    beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 49 ARRB2
    beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] 2222 BCMO1 221.509 220.108 1.00637
    beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 2221 no value
    beta-catenin (pro2286). [swissprot;acc:p35222] 801 CTNNB1 224.445 214.894 1.04445
    beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] 1510 ACTR1B 225.148 221.177 1.01795
    beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] 808 NAPB 212.386 221.785 1.04425
    beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1] 3145 UPB1 0.00001 0.00001 1
    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 241.373 267.352 1.10763
    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 221.022 221.116 1.00043
    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 223.58 235.027 1.0512
    bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] 1848 BAAT 218.441 216.064 1.011
    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 218.436 215.553 1.01337
    block 23. [sptrembl;acc:q8nhw5] 1091 no value 226.205 232.858 1.02941
    block of proliferation 1. [swissprot;acc:q14137] 512 BOP1 250.794 234.433 1.06979
    blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 1930 no value 196.964 198.935 1.01001
    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 215.673 212.971 1.01269
    bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] 793 SERPINB10 224.244 234.511 1.04578
    bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003] 3069 BMP5 0.00001 0.00001 1
    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 210.586 208.803 1.00854
    brain protein 16. [refseq;acc:nm_016458] 1847 no value 216.811 219.195 1.011
    brain protein 44. [swissprot;acc:o95563] 742 BRP44 126.215 120.078 1.05111
    branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 2672 BCAT1 210.957 210.741 1.00102
    branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 2687 BCAT2 210.939 210.755 1.00087
    brca1 associated protein. [refseq;acc:nm_006768] 3161 BRAP 0.00001 0.00001 1
    brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 1752 BARD1 216.271 218.991 1.01258
    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 240.782 265.717 1.10356
    breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 229 BCAR3 226.401 202.094 1.12028
    breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 939 BRCA1 216.501 224.27 1.03588
    breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 691 BCAS2 217.602 206.195 1.05532
    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 220.521 220.395 1.00057

    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/