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 red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 7386 to 7435 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    4158 ANK2 ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] 202.624 200.519 1.0105
    4159 PRKACB camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] 198.273 196.216 1.01048
    4160 PRKACA camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] 198.28 196.223
    4161 PRKACG camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 198.254 196.202 1.01046
    4162 no value c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 207.355 209.52 1.01044
    4163 CDH1 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 207.356
    4164 FOXC2 forkhead box protein c2 (forkhead-related protein fkhl14) (mesenchyme fork head protein 1) (mfh-1 protein) (transcription factor fkh-14). [swissprot;acc:q99958] 207.478 205.337 1.01043
    4165 CCT6B t-complex protein 1, zeta-2 subunit (tcp-1-zeta-2) (cct-zeta-2) (tcp- 1-zeta-like) (cct-zeta-like) (testis-specific tcp20) (testis-specific protein tsa303). [swissprot;acc:q92526] 199.886 197.823
    4166 FOXC1 forkhead box protein c1 (forkhead-related protein fkhl7) (forkhead- related transcription factor 3) (freac-3). [swissprot;acc:q12948] 207.478 205.337
    4167 no value 60s ribosomal protein l23a. [swissprot;acc:p29316] 207.351 209.511 1.01042
    4168 LETM1 leucine zipper-ef-hand containing transmembrane protein 1. [refseq;acc:nm_012318] 205.583 203.462
    4169 SIAH2 seven in absentia homolog 2. [refseq;acc:nm_005067] 202.616 200.529 1.01041
    4170 CCT6A t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] 199.894 197.836 1.0104
    4171 NMUR1 g protein-coupled receptor 66. [refseq;acc:nm_006056] 199.766 197.712 1.01039
    4172 SURF4 surfeit locus protein 4. [swissprot;acc:o15260] 202.633 200.55
    4173 NMUR2 neuromedin u receptor 2. [refseq;acc:nm_020167] 199.766 197.712
    4174 CLPTM1L cisplatin resistance related protein crr9p. [refseq;acc:nm_030782]
    4175 PRKX protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] 198.106 196.07 1.01038
    4176 FOXL1 forkhead box protein l1 (forkhead-related protein fkhl11) (forkhead- related transcription factor 7) (freac-7). [swissprot;acc:q12952] 207.523 205.392
    4177 FOXA1 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 205.411 203.301
    4178 no value seven in absentia homolog 1. [refseq;acc:nm_003031] 202.646 200.567 1.01037
    4179 RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] 207.337 209.485 1.01036
    4180 FOXD2 forkhead box protein d2 (forkhead-related protein fkhl17) (forkhead- related transcription factor 9) (freac-9). [swissprot;acc:o60548] 207.544 205.417 1.01035
    4181 FOXA2 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] 205.289 203.186
    4182 FOXD3 forkhead box protein d3 (hnf3/fh transcription factor genesis). [swissprot;acc:q9uju5] 207.55 205.425 1.01034
    4183 no value forkhead box protein d4b (myeloid factor-gamma). [swissprot;acc:q8wxt5] 207.554 205.43
    4184 FOXD4 forkhead box protein d4-like 1. [swissprot;acc:q9nu39] 207.55 205.425
    4185 FOXE3 forkhead box protein e3 (forkhead-related protein fkhl12) (forkhead- related transcription factor 8) (freac-8). [swissprot;acc:q13461] 207.557 205.434 1.01033
    4186 FOXD4L1 forkhead box protein d4 (forkhead-related protein fkhl9) (forkhead- related transcription factor 5) (freac-5) (myeloid factor-alpha). [swissprot;acc:q12950] 207.561 205.439
    4187 RECQL5 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] 202.438 200.37 1.01032
    4188 FOXL2 forkhead box protein l2. [swissprot;acc:p58012] 207.578 205.46 1.01031
    4189 FOXB1 forkhead box protein b1 (transcription factor fkh-5). [swissprot;acc:q99853] 207.575 205.456
    4190 FOXI1 forkhead box protein i1 (forkhead-related protein fkhl10) (forkhead- related transcription factor 6) (freac-6) (hepatocyte nuclear factor 3 forkhead homolog 3) (hnf-3/fork-head homolog-3) (hfh-3). [swissprot;acc:q12951] 207.59 205.474 1.0103
    4191 FOXF2 forkhead box protein f2 (forkhead-related protein fkhl6) (forkhead- related transcription factor 2) (freac-2) (forkhead-related activator- 2). [swissprot;acc:q12947] 207.597 205.483 1.01029
    4192 FOXF1 forkhead box protein f1 (forkhead-related protein fkhl5) (forkhead- related transcription factor 1) (freac-1) (forkhead-related activator- 1). [swissprot;acc:q12946]
    4193 DEAF1 deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] 203.508 201.442 1.01026
    4194 NUP107 nuclear pore complex protein nup107 (nucleoporin nup107) (107 kda nucleoporin). [swissprot;acc:p57740] 195.357 193.375 1.01025
    4195 REEP5 polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] 200.974 198.937 1.01024
    4196 RFXANK dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] 203.591 201.529 1.01023
    4197 FOXQ1 forkhead box protein q1 (hepatocyte nuclear factor 3 forkhead homolog 1) (hnf-3/forkhead-like protein 1) (hfh-1). [swissprot;acc:q9c009] 207.659 205.56 1.01021
    4198 PPT1 palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] 203.592 201.534
    4199 RABAC1 rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] 202.011 199.969
    4200 CCNC cyclin c. [swissprot;acc:p24863] 199.253 197.241 1.0102
    4201 CLCN5 chloride channel protein 5 (clc-5). [swissprot;acc:p51795] 203.636 201.582 1.01019
    4202 FOXJ1 forkhead box protein j1 (forkhead-related protein fkhl13) (hepatocyte nuclear factor 3 forkhead homolog 4) (hfh-4). [swissprot;acc:q92949] 207.68 205.585
    4203 ANKRA2 ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] 203.592 201.541 1.01018
    4204 CLCN4 chloride channel protein 4 (clc-4). [swissprot;acc:p51793] 203.637 201.584
    4205 CLCN3 chloride channel protein 3 (clc-3). [swissprot;acc:p51790] 203.646 201.595 1.01017
    4206 MYC myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] 203.698 201.652 1.01015
    4207 MED30 trap/mediator complex component trap25. [refseq;acc:nm_080651] 200.981 198.966 1.01013

    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/