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 [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3101 to 3150 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    776 no value dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Divided High confidence 225.996 215.535 1.04854
    ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Subtracted Low confidence 208.488 203.181 5.307
    MAD1L1 mad1-like 1; mad1 (mitotic arrest deficient, yeast, homolog)-like 1; mitotic-arrest deficient 1, yeast, homolog-like 1; tumor protein p53 inducible protein 9. [refseq;acc:nm_003550] Divided 208.017 202.601 1.02673
    SQSTM1 sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Subtracted High confidence 221.965 212.404 9.561
    777 AP1S3 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] Divided Low confidence 204.807 199.484 1.02668
    HDAC1 histone deacetylase 1 (hd1). [swissprot;acc:q13547] High confidence 225.989 215.53 1.04853
    PPP1R3B protein phosphatase 1, regulatory (inhibitor) subunit 3b. [refseq;acc:nm_024607] Subtracted Low confidence 203.48 198.181 5.299
    SCP2 nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] High confidence 221.965 212.404 9.561
    778 CDC25A m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Low confidence 207.541 202.25 5.291
    CTNNB1 beta-catenin (pro2286). [swissprot;acc:p35222] High confidence 224.445 214.894 9.551
    SNX6 sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Divided 209.191 219.332 1.04848
    WDR26 wd repeat domain 26. [refseq;acc:nm_025160] Low confidence 188.145 183.258 1.02667
    779 no value importin 9. [refseq;acc:nm_018085] Subtracted 204.192 198.902 5.29
    ABI2 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] Divided 202.48 197.229 1.02662
    DCTD deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] High confidence 230.516 241.641 1.04826
    PARK2 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Subtracted 231.734 222.222 9.512
    780 no value hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
    importin 9. [refseq;acc:nm_018085] Divided Low confidence 204.192 198.902 1.0266
    HMBS porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Subtracted 204.238 198.951 5.287
    POLR2F dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] Divided High confidence 232.762 243.933 1.04799
    781 no value cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Subtracted 231.734 222.222 9.512
    MRTO4 ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Divided 245.84 257.636 1.04798
    PRMT7 protein arginine n-methyltransferase (ec 2.1.1.-). [swissprot;acc:q9nvm4] Low confidence 203.591 198.319 1.02658
    Subtracted 5.272
    782 no value translin. [swissprot;acc:q15631] Divided High confidence 224.385 235.131 1.04789
    PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Low confidence 203.591 198.319 1.02658
    Subtracted 5.272
    PSIP1 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] High confidence 231.734 222.222 9.512
    783 HMBS porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Divided Low confidence 204.238 198.951 1.02657
    KRR1 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Subtracted 204.204 198.939 5.265
    RPL8 60s ribosomal protein l8. [swissprot;acc:p25120] High confidence 231.734 222.222 9.512
    TSNAX translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Divided 224.385 235.131 1.04789
    784 HDGF hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Subtracted 231.734 222.222 9.512
    PQBP1 polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] Divided 224.385 235.131 1.04789
    SPTLC1 serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Subtracted Low confidence 207.116 201.851 5.265
    XAB2 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Divided 201.338 196.126 1.02657
    785 ABI1 spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] 202.469 197.233 1.02655
    HDGFL1 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Subtracted High confidence 231.734 222.222 9.512
    NET1 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Divided 244.447 233.508 1.04685
    SLC30A1 zinc transporter 1 (znt-1). [swissprot;acc:q9y6m5] Subtracted Low confidence 206.173 200.909 5.264
    786 ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 200.18 194.922 5.258
    ARHGEF3 rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Divided High confidence 244.447 233.508 1.04685
    DDX6 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Subtracted 231.734 222.222 9.512
    FBXL11 f-box and leucine-rich repeat protein 11; f-box protein fbl11. [refseq;acc:nm_012308] Divided Low confidence 202.957 208.337 1.02651
    787 ATP6V1C2 atpase, h+ transporting, lysosomal 42kda, v1 subunit c isoform 2; v-atpase c2 subunit. [refseq;acc:nm_144583] 202.489 197.259
    STX1A syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Subtracted 210.979 205.723 5.256
    TMEM131 rw1 protein (fragment). [swissprot;acc:q92545] High confidence 231.734 222.222 9.512
    UTP20 down-regulated in metastasis. [refseq;acc:nm_014503] Divided 244.447 233.508 1.04685
    788 EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Low confidence 200.788 195.605 1.0265
    LOH12CR1 loh1cr12. [refseq;acc:nm_058169] Subtracted High confidence 230.087 220.579 9.508

    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/