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 [...,...].
    Gene Hugo Rank Value Type description Network Comparison Type Filtered green red Interaction Map network_comparison
    Results: HTML CSV LaTeX Showing element 327 to 376 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Interaction Map  : High confidence
    Hugo
    		Rank
    		description
    		green
    		red
    		network_comparison
    ABCD3 2166 atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] 214.481 215.925 1.00673
    ABHD1 1961 alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] 213.703 211.633 1.00978
    ABHD2 1935 abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] 216.279 218.43 1.00995
    ABHD3 1959 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] 213.703 211.633 1.00978
    ABI1 1846 spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] 214.698 217.066 1.01103
    ABI2 1845 abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] 214.702 217.077 1.01106
    ABL1 553 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 194.346 207.26 1.06645
    ABL2 548 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]
    ABLIM1 668 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] 216.576 229.072 1.0577
    ABLIM2 660 actin binding lim protein 2. [refseq;acc:nm_032432]
    ABT1 1169 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] 213.784 219.399 1.02626
    ACAA1 2300 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 192.541 191.563 1.00511
    ACACA 2319 acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 195.8 194.842 1.00492
    ACACB 2315 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 195.787 194.825 1.00494
    ACADM 1413 acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] 210.42 206.102 1.02095
    ACADVL 733 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 155.961 164 1.05154
    ACAT1 2306 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] 192.544 191.571 1.00508
    ACBD3 1177 golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] 212.672 218.186 1.02593
    ACLY 2689 atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] 213.619 213.792 1.00081
    ACO1 2696 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] 201.794 201.652 1.0007
    ACOT1 1849 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] 216.074 218.445 1.01097
    ACOT4 1851 peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] 216.08 218.448 1.01096
    ACOT9 2011 putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] 191.766 193.517 1.00913
    ACOX1 2643 acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067] 194.328 194.097 1.00119
    ACOX2 2404 acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] 194.105 193.389 1.0037
    ACP1 2707 red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] 215.232 215.096 1.00063
    ACRC 2101 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 213.27 211.71 1.00737
    ACSS2 2039 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] 192.191 190.551 1.00861
    ACTG1 1529 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 213.031 216.762 1.01751
    ACTN1 1806 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] 214.482 217.009 1.01178
    ACTN2 1799 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] 214.481 217.016 1.01182
    ACTN4 1805 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] 214.482 217.008 1.01178
    ACTR1A 1509 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 221.177 225.148 1.01795
    ACTR1B 1510 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025]
    ACTR2 2626 actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142] 225.195 224.891 1.00135
    ACTR3 2631 actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
    ACTR3B 2628 similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]
    ACVR1 3050 activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771] 0.00001 0.00001 1
    ACVR1B 1364 serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] 228.797 223.885 1.02194
    ACVR1C 1366 activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] 228.795 223.884
    ACVRL1 2952 serine/threonine-protein kinase receptor r3 precursor (ec 2.7.1.37) (skr3) (activin receptor-like kinase 1) (alk-1) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:p37023] 0.00001 0.00001 1
    ACY1 1420 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] 208.229 203.979 1.02084
    ADAMTS9 2516 adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] 216.341 215.835 1.00234
    ADC 2054 ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] 205.948 207.665 1.00834
    ADCK1 1733 aarf domain containing kinase 1. [refseq;acc:nm_020421] 212.567 215.336 1.01303
    ADCK2 1731 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853]
    ADCK4 1732 aarf domain containing kinase 4. [refseq;acc:nm_024876]
    ADCY5 467 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 267.226 248.152 1.07686
    ADCY6 466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
    ADD1 1965 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 222.258 224.432 1.00978

    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/