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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1030 to 1079 of 12912 in total
    Network Comparison Type	Divided
    Interaction Map High confidence
    Filtered 1
    Rank description Value Type red green network_comparison 258 huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291] Squared 76438 58889.7 1.29799 258 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582] Ranked 227.999 204.366 1.11564 258 thrombospondin 3 precursor. [source:swissprot;acc:p49746] Rooted 51.6132 45.8422 1.12589 259 goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [source:swissprot;acc:q9y5p4] Squared 76360.8 58841.7 1.29773 259 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300] Ranked 227.999 204.37 1.11562 259 neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401] Measured 6417.81 7852.52 1.22355 259 tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9] Rooted 58.2964 65.5926 1.12516 260 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5] Ranked 219.421 196.978 1.11394 260 huntingtin interacting protein 1 related (hip1-related) (hip 12). [source:swissprot;acc:o75146] Squared 76296.4 58801.6 1.29752 260 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904] Rooted 59.0951 66.4332 1.12417 260 signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458] Measured 4244.95 5193.42 1.22343 261 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042] Ranked 219.421 196.978 1.11394 261 pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [source:swissprot;acc:p11498] Squared 48127.9 62245.6 1.29334 261 ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713] Rooted 62.3337 70.0738 1.12417 261 signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458] Measured 4247.36 5192.61 1.22255 262 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [source:refseq;acc:nm_006693] Measured 24896.4 20431.7 1.21852 262 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041] Ranked 219.421 196.978 1.11394 262 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544] Squared 26157.6 20236.2 1.29261 262 polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195] Rooted 59.4073 66.7002 1.12276 263 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306] Squared 26157.6 20236.2 1.29261 263 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043] Ranked 219.421 196.978 1.11394 263 paxillin. [source:swissprot;acc:p49023] Rooted 59.4073 66.7002 1.12276 263 trs85 homolog. [source:swissprot;acc:q9y2l5] Measured 24896.4 20431.7 1.21852 264 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622] Squared 26157.6 20236.2 1.29261 264 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653] Measured 4987.58 4094.57 1.2181 264 mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026] Ranked 219.421 196.978 1.11394 264 wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768] Rooted 66.1122 74.1438 1.12148 265 leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66] Squared 26157.6 20236.2 1.29261 265 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533] Ranked 225.217 202.459 1.11241 265 u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777] Rooted 56.031 62.8281 1.12131 265 wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8] Measured 24806.9 20369.9 1.21782 266 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570] Measured 24806.9 20369.9 1.21782 266 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322] Squared 26157.6 20236.2 1.29261 266 proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108] Rooted 66.1064 74.1074 1.12103 266 transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477] Ranked 241.07 267.88 1.11121 267 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583] Ranked 241.07 267.88 1.11121 267 leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71] Squared 26157.6 20236.2 1.29261 267 ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967] Measured 14021.4 11523 1.21682 267 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684] Rooted 66.1064 74.1073 1.12103 268 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0] Measured 24473.9 20127.8 1.21593 268 eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010] Ranked 271.016 244.167 1.10996 268 laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047] Squared 26157.6 20236.2 1.29261 268 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931] Rooted 66.1064 74.1074 1.12103 269 cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585] Ranked 241.373 267.352 1.10763 269 thymic stromal co-transporter. [source:refseq;acc:nm_033051] Squared 26157.6 20236.2 1.29261 269 tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631] Rooted 66.1064 74.1074 1.12103 269 u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777] Measured 4590.18 5575.52 1.21466 270 crk-like protein. [source:swissprot;acc:p46109] Rooted 66.1064 74.1074 1.12103 270 fad synthetase. [source:refseq;acc:nm_025207] Ranked 241.373 267.352 1.10763 270 fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917] Measured 23640.2 19479.8 1.21358 Legend: - Rank is the rank after comparing the two networks - 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/