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 Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 780 to 829 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    195 RAB11FIP3 Subtracted eferin. [swissprot;acc:o75154] 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 Divided forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 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 Subtracted associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 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 Divided forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 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 Subtracted 60s ribosomal protein l32. [swissprot;acc:p02433] 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 Divided forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 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 Subtracted 60s ribosomal protein l27. [swissprot;acc:p08526] 211.912 10.356 201.556
    199 CRYAA Divided alpha crystallin a chain. [swissprot;acc:p02489] 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 Subtracted general transcription factor iiic, polypeptide 3, 102kda; general transcription factor iiic, polypeptide 3 (102kd); transcription factor iiic, 102 kd. [refseq;acc:nm_012086] 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 Divided alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] 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 Subtracted 60s ribosomal protein l11. [swissprot;acc:p39026] High confidence 241.828 25.518 267.346
    SF4 Divided splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 240.133 1.13601 211.382
    UBE2E1 Subtracted ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Low confidence 203.935 10.154 214.089
    202 GNG4 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 211.51 1.05079 222.252
    RPS4Y2 Subtracted 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] High confidence 240.758 25.321 266.079
    TRPC4 Divided short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 201.478 1.13553 228.784
    XKR7 Subtracted dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Low confidence 178.507 10.136 168.371
    203 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] High confidence 240.758 25.32 266.078
    GNG3 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Low confidence 211.506 1.05076 222.243
    TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] High confidence 201.515 1.13516 228.752
    TENC1 Subtracted 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] Low confidence 216.404 10.127 206.277
    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 25.044 243.588
    GNG8 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Low confidence 211.484 1.05065 222.196
    TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] High confidence 201.515 1.13516 228.752
    UBE2E4P Subtracted ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Low confidence 203.933 10.126 214.059
    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 25.043 243.592
    GNG5 Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Low confidence 211.475 1.05061 222.177
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] High confidence 228.1 1.13501 200.968
    TIMM23 Subtracted mitochondrial import inner membrane translocase subunit tim23. [swissprot;acc:o14925] Low confidence 220.722 10.077 210.645
    206 no value Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 211.457 1.05051 222.138
    FMO6P Subtracted putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] 209.792 10.034 199.758
    LUC7L Divided luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] High confidence 228.085 1.13472 201.006
    RPS15A Subtracted 40s ribosomal protein s15a. [swissprot;acc:p39027] 241.411 25.003 266.414
    207 ANAPC10 Divided anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Low confidence 213.495 1.05044 203.244
    EIF4G3 Subtracted eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] High confidence 237.312 24.949 212.363
    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 10.021 199.761
    PSEN2 Divided presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] High confidence 285.684 1.13261 252.234
    208 no value Subtracted 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 240.782 24.935 265.717

    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/