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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 475 to 524 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
238 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Divided 27642.5 22440.4 1.23182
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Subtracted 9649.61 11053.5 1403.89
239 carboxypeptidase b precursor. [refseq;acc:nm_020361] Divided 7711.38 6265.8 1.23071
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Subtracted 9649.61 11053.5 1403.89
240 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Divided 7711.36 6265.79 1.23071
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Subtracted 9649.61 11053.5 1403.89
241 mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Divided 7711.31 6265.76 1.23071
242 max protein. [swissprot;acc:p25912] 4640.26 5704.87 1.22943
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Subtracted 9649.61 11053.5 1403.89
243 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Divided 4246.95 5208.98 1.22652
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Subtracted 9649.61 11053.5 1403.89
244 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided 4250.14 5211.25 1.22614
245 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 4251.65 5212.33 1.22595
methyltransferase like 2. [refseq;acc:nm_018396] Subtracted 13241.4 11864 1377.4
246 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Divided 4252.66 5213.05 1.22583
247 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Subtracted 13241.4 11864 1377.4
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Divided 6416.68 7865.15 1.22574
248 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Subtracted 13241.4 11864 1377.4
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Divided 6417.18 7859.6 1.22477
249 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Subtracted 4405.4 5782.08 1376.68
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Divided 6417.18 7859.59 1.22477
250 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 7859.6
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Subtracted 4578.09 5939.91 1361.82
251 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 4579.34 5940.64 1361.3
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Divided 6417.18 7859.6 1.22477
252 crk-like protein. [swissprot;acc:p46109]
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Subtracted 9648.27 10994.9 1346.63
253 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 9642.22 10986.4 1344.18
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Divided 6417.18 7859.59 1.22477
254 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Subtracted 9634.98 10976.2 1341.22
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Divided 6417.18 7859.6 1.22477
255 mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 4455.95 5774.03 1318.08
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Divided 6417.18 7859.6 1.22477
256 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] 6417.19 7859.51 1.22476
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Subtracted 4456.67 5773.77 1317.1
257 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Divided 6417.31 7858.12 1.22452
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Subtracted 4456.93 5773.67 1316.74
258 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Divided 6417.33 7857.93 1.22449
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Subtracted 4457.06 5773.63 1316.57
259 neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Divided 6417.81 7852.52 1.22355
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Subtracted 4569.48 5885.79 1316.31
260 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 12515.4 11221.1 1294.3
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 4244.95 5193.42 1.22343
261 4247.36 5192.61 1.22255
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Subtracted 4571.89 5864.86 1292.97
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. [refseq;acc:nm_006693] Divided 24896.4 20431.7 1.21852
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 4571.89 5864.86 1292.97

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
- 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/