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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 758 to 807 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    190 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 1.0524 200.074
    GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Subtracted 211.383 10.593 221.976
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Divided High confidence 226.582 1.14179 198.444
    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 25.979 267.352
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 226.582 1.14179 198.444
    PXK px serine/threonine kinase. [refseq;acc:nm_017771] Subtracted Low confidence 196.372 10.575 206.947
    SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Divided 201.43 1.05224 191.43
    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 10.575 206.947
    LGTN ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] High confidence 241.373 25.979 267.352
    MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Divided 227.491 1.14055 199.458
    RC3H2 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Low confidence 217.341 1.05214 206.571
    193 HBS1L hbs1-like. [refseq;acc:nm_006620] 206.166 1.05213 216.913
    MSI1 musashi 1. [refseq;acc:nm_002442] High confidence 227.491 1.14055 199.458
    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 25.979 267.352
    TSGA10 testis specific, 10. [refseq;acc:nm_025244] Low confidence 196.373 10.573 206.946
    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 1.05207 205.046
    POR nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Subtracted High confidence 241.373 25.979 267.352
    RAB11FIP4 rab11-family interacting protein 4. [refseq;acc:nm_032932] Low confidence 183.27 10.568 172.702
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Divided High confidence 227.491 1.14055 199.458
    195 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Low confidence 211.679 1.0517 222.623
    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 25.979 267.352
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Divided 227.971 1.13748 200.417
    RAB11FIP3 eferin. [swissprot;acc:o75154] Subtracted Low confidence 183.27 10.568 172.702
    196 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] High confidence 272.781 25.889 246.892
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Divided 263.215 1.13745 231.407
    GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Low confidence 211.679 1.0517 222.623
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Subtracted 196.381 10.54 206.921
    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 10.483 200.074
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Divided High confidence 263.215 1.13745 231.407
    RPL27 60s ribosomal protein l27. [swissprot;acc:p08526] Low confidence 211.912 1.05138 201.556
    SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] Subtracted High confidence 241.13 25.839 266.969
    198 no value 40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 25.793 267.642
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Divided 263.191 1.13741 231.394
    HSPB6 heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] Low confidence 219.606 1.05123 208.904
    RPL27 60s ribosomal protein l27. [swissprot;acc:p08526] Subtracted 211.912 10.356 201.556
    199 CRYAA alpha crystallin a chain. [swissprot;acc:p02489] Divided 219.589 1.05119 208.895
    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 1.13729 276.059
    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 10.302 206.926
    RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] High confidence 241.399 25.689 267.088
    200 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 25.527 267.335
    ANAPC10 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Low confidence 213.495 10.251 203.244
    CRYAB alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] Divided 219.543 1.05111 208.868
    EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] High confidence 242.718 1.1372 276.018
    201 CYC1 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Low confidence 208.591 1.051 219.23
    RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Subtracted High confidence 241.828 25.518 267.346
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 240.133 1.13601 211.382
    UBE2E1 ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Subtracted Low confidence 203.935 10.154 214.089
    202 GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided 211.51 1.05079 222.252
    RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted High confidence 240.758 25.321 266.079
    TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 201.478 1.13553 228.784

    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/