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 green network_comparison
    Results: HTML CSV LaTeX Showing element 2958 to 3007 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    trophinin. [swissprot;acc:q12816] 103 TRO 88.2482 110.265 1.24949
    tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] 2334 TMOD1 229.258 230.294 1.00452
    tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] 2945 TPM1 0.00001 0.00001 1
    tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] 2931 TPM3
    tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] 2833 TPM4
    trs85 homolog. [swissprot;acc:q9y2l5] 851 KIAA1012 107.842 112.329 1.04161
    trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 431 TRUB1 236.245 255.113 1.07987
    tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] 1663 TDO2 218.335 215.26 1.01429
    tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] 2261 WARS 221.599 220.351 1.00566
    tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] 2263 WARS2
    tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] 2646 TSC22D4 213.169 213.417 1.00116
    tu12b1-ty protein. [refseq;acc:nm_016575] 3074 NT5DC3 0.00001 0.00001 1
    tubby protein homolog. [swissprot;acc:p50607] 966 TUB 211.987 204.964 1.03426
    tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] 970 TULP1
    tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] 973 TULP3
    tubulin alpha-3/alpha-7 chain (alpha-tubulin 3/7). [swissprot;acc:p05214] 3175 TUBA3D 0.00001 0.00001 1
    tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] 1739 TUBG1 206.595 209.258 1.01289
    tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3] 1742 TUBG2
    tubulin tyrosine ligase-like protein 1. [swissprot;acc:o95922] 3141 TTLL1 0.00001 0.00001 1
    tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] 2543 BRPF1 224.726 225.164 1.00195
    tubulin-specific chaperone a (tubulin-folding cofactor a) (cfa) (tcp1-chaperonin cofactor a). [swissprot;acc:o75347] 2817 TBCA 0.00001 0.00001 1
    tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] 2010 TBCC 193.517 191.766 1.00913
    tubulin-tyrosine ligase. [refseq;acc:nm_153712] 1853 TTL 217.924 215.564 1.01095
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 421 TFIP11 223.202 205.9 1.08403
    tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] 1980 SERINC1 209.539 207.529 1.00969
    tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] 1979 SERINC3
    tumor differentially expressed protein 2. [refseq;acc:nm_178865] 1978 SERINC2
    tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] 2472 TNS3 218.218 217.564 1.00301
    tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] 1203 TNFAIP1 219.023 213.606 1.02536
    tumor protein d52 (n8 protein). [swissprot;acc:p55327] 1223 TPD52 206.771 211.926 1.02493
    tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] 1222 TPD52L1 206.774 211.936 1.02496
    tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] 1301 TPD52L2 206.852 211.757 1.02371
    tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] 2295 TP53BP2 162.86 163.712 1.00523
    tumor susceptibility gene 101 protein. [swissprot;acc:q99816] 2202 TSG101 195.97 194.7 1.00652
    twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] 2182 PEO1 218.062 216.624 1.00664
    type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 1953 PPP1R2P9 125.912 127.146 1.0098
    tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] 1033 TYR 221.183 214.406 1.03161
    tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 1019 TYRL 221.302 214.409 1.03215
    tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 1562 no value 167.687 170.455 1.01651
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 548 ABL2 207.26 194.346 1.06645
    tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 656 FRK 216.504 204.622 1.05807
    tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 550 HCK 207.26 194.346 1.06645
    tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [swissprot;acc:p34925] 2858 RYK 0.00001 0.00001 1
    tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] 711 YARS 232.468 245.048 1.05411
    u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 190 SNRP70 226.582 198.444 1.14179
    u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 453 SNRPA1 224.161 207.972 1.07784
    u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 751 no value 223.463 212.875 1.04974
    u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] 2002 SNRPB2 214.775 216.769 1.00928
    u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] 1199 MPHOSPH10 241.496 235.508 1.02543
    u3 snornp protein 4 homolog. [refseq;acc:nm_033416] 821 IMP4 221.676 231.453 1.0441

    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/