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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 751 to 800 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    Hugo
    description
    Network Comparison Type
    Interaction Map
    red
    green
    network_comparison
    188 PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided High confidence 226.582 198.444 1.14179
    RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Low confidence 189.45 179.944 1.05283
    189 DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 214.779 204.039 1.05264
    PCYT1A cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Subtracted High confidence 241.373 267.352 25.979
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Divided 226.582 198.444 1.14179
    STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Subtracted Low confidence 196.362 206.979 10.617
    190 FLAD1 fad synthetase. [refseq;acc:nm_025207] High confidence 241.373 267.352 25.979
    FMO5 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Divided Low confidence 210.557 200.074 1.0524
    GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Subtracted 211.383 221.976 10.593
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Divided High confidence 226.582 198.444 1.14179
    191 no value 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] Subtracted 241.373 267.352 25.979
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 226.582 198.444 1.14179
    PXK px serine/threonine kinase. [refseq;acc:nm_017771] Subtracted Low confidence 196.372 206.947 10.575
    SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Divided 201.43 191.43 1.05224
    192 no value bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] Subtracted 196.372 206.947 10.575
    LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] High confidence 241.373 267.352 25.979
    MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Divided 227.491 199.458 1.14055
    RC3H2 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Low confidence 217.341 206.571 1.05214
    193 HBS1L hbs1-like. [refseq;acc:nm_006620] 206.166 216.913 1.05213
    MSI1 musashi 1. [refseq;acc:nm_002442] High confidence 227.491 199.458 1.14055
    PAPSS1 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] Subtracted 241.373 267.352 25.979
    TSGA10 testis specific, 10. [refseq;acc:nm_025244] Low confidence 196.373 206.946 10.573
    194 COG5 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Divided 215.723 205.046 1.05207
    POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Subtracted High confidence 241.373 267.352 25.979
    RAB11FIP4 rab11-family interacting protein 4. [refseq;acc:nm_032932] Low confidence 183.27 172.702 10.568
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Divided High confidence 227.491 199.458 1.14055
    195 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Low confidence 211.679 222.623 1.0517
    PCYT1B cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Subtracted High confidence 241.373 267.352 25.979
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Divided 227.971 200.417 1.13748
    RAB11FIP3 eferin. [swissprot;acc:o75154] Subtracted Low confidence 183.27 172.702 10.568
    196 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] High confidence 272.781 246.892 25.889
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Divided 263.215 231.407 1.13745
    GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Low confidence 211.679 222.623 1.0517
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Subtracted 196.381 206.921 10.54
    197 FMO5 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] 210.557 200.074 10.483
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Divided High confidence 263.215 231.407 1.13745
    RPL27 60s ribosomal protein l27. [swissprot;acc:p08526] Low confidence 211.912 201.556 1.05138
    SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] Subtracted High confidence 241.13 266.969 25.839
    198 no value 40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 267.642 25.793
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Divided 263.191 231.394 1.13741
    HSPB6 heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] Low confidence 219.606 208.904 1.05123
    RPL27 60s ribosomal protein l27. [swissprot;acc:p08526] Subtracted 211.912 201.556 10.356
    199 CRYAA alpha crystallin a chain. [swissprot;acc:p02489] Divided 219.589 208.895 1.05119
    EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] High confidence 242.735 276.059 1.13729
    GTF3C3 general transcription factor iiic, polypeptide 3, 102kda; general transcription factor iiic, polypeptide 3 (102kd); transcription factor iiic, 102 kd. [refseq;acc:nm_012086] Subtracted Low confidence 217.228 206.926 10.302
    RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] High confidence 241.399 267.088 25.689
    200 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 267.335 25.527
    ANAPC10 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Low confidence 213.495 203.244 10.251
    CRYAB alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] Divided 219.543 208.868 1.05111
    EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] High confidence 242.718 276.018 1.1372

    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/