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 782 to 831 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    196 FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Divided High confidence 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
    201 CYC1 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Low confidence 208.591 219.23 1.051
    RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Subtracted High confidence 241.828 267.346 25.518
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 240.133 211.382 1.13601
    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 203.935 214.089 10.154
    202 GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided 211.51 222.252 1.05079
    RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted High confidence 240.758 266.079 25.321
    TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 201.478 228.784 1.13553
    XKR7 dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Subtracted Low confidence 178.507 168.371 10.136
    203 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] High confidence 240.758 266.078 25.32
    GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Divided Low confidence 211.506 222.243 1.05076
    TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] High confidence 201.515 228.752 1.13516
    TENC1 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] Subtracted Low confidence 216.404 206.277 10.127
    204 CAPN2 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] High confidence 268.632 243.588 25.044
    GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Divided Low confidence 211.484 222.196 1.05065
    TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] High confidence 201.515 228.752 1.13516
    UBE2E4P ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Subtracted Low confidence 203.933 214.059 10.126
    205 CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] High confidence 268.635 243.592 25.043
    GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Divided Low confidence 211.475 222.177 1.05061
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] High confidence 228.1 200.968 1.13501
    TIMM23 mitochondrial import inner membrane translocase subunit tim23. [swissprot;acc:o14925] Subtracted Low confidence 220.722 210.645 10.077
    206 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided 211.457 222.138 1.05051
    FMO6P putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Subtracted 209.792 199.758 10.034
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Divided High confidence 228.085 201.006 1.13472
    RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] Subtracted 241.411 266.414 25.003
    207 ANAPC10 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Divided Low confidence 213.495 203.244 1.05044
    EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Subtracted High confidence 237.312 212.363 24.949
    FMO2 dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Low confidence 209.782 199.761 10.021
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided High confidence 285.684 252.234 1.13261
    208 no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Subtracted 240.782 265.717 24.935
    FMO3 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Low confidence 209.778 199.757 10.021
    FMO6P putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Divided 209.792 199.758 1.05023

    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/