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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Value Type Rank Gene Network Comparison Type Interaction Map green description red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 25824 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
green
description
red
network_comparison
226 Divided 7279.6 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 9035 1.24114
Subtracted 7858.12 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 6417.31 1440.81
227 Divided 7279.6 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 9035 1.24114
Subtracted 7857.93 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 6417.33 1440.6
228 Divided 7279.6 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 9035 1.24114
Subtracted 7852.52 neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 6417.81 1434.71
229 Divided 7279.6 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 9035 1.24114
Subtracted 11846.2 small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] 10434.4 1411.8
230 Divided 7279.6 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 9035 1.24114
Subtracted 11053.5 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] 9649.61 1403.89
231 Divided 7279.6 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 9035 1.24114
Subtracted 11053.5 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 9649.61 1403.89
232 Divided 7279.6 dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 9035 1.24114
Subtracted 11053.5 udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] 9649.61 1403.89
233 Divided 7279.6 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 9035 1.24114
Subtracted 11053.5 rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] 9649.61 1403.89
234 Divided 6410.58 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 5181.2 1.23728
Subtracted 11053.5 map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] 9649.61 1403.89
235 Divided 6410.58 ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 5181.2 1.23728
Subtracted 11053.5 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] 9649.61 1403.89
236 Divided 5828.46 spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 4723.53 1.23392
Subtracted 11053.5 nitrogen fixation cluster-like. [refseq;acc:nm_014301] 9649.61 1403.89
237 Divided 5631.2 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 4567.04 1.23301
Subtracted 11053.5 star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] 9649.61 1403.89
238 Divided 22440.4 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 27642.5 1.23182
Subtracted 11053.5 star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] 9649.61 1403.89
239 Divided 6265.8 carboxypeptidase b precursor. [refseq;acc:nm_020361] 7711.38 1.23071
Subtracted 11053.5 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 9649.61 1403.89
240 Divided 6265.79 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 7711.36 1.23071
Subtracted 11053.5 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 9649.61 1403.89
241 Divided 6265.76 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 7711.31 1.23071
Subtracted 11053.5 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] 9649.61 1403.89
242 Divided 5704.87 max protein. [swissprot;acc:p25912] 4640.26 1.22943
Subtracted 11053.5 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 9649.61 1403.89
243 Divided 5208.98 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 4246.95 1.22652
Subtracted 11053.5 neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 9649.61 1403.89
244 Divided 5211.25 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 4250.14 1.22614
Subtracted 11053.5 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 9649.61 1403.89
245 Divided 5212.33 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 4251.65 1.22595
Subtracted 11864 methyltransferase like 2. [refseq;acc:nm_018396] 13241.4 1377.4
246 Divided 5213.05 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 4252.66 1.22583
Subtracted 11864 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] 13241.4 1377.4
247 Divided 7865.15 wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 6416.68 1.22574
Subtracted 11864 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 13241.4 1377.4
248 Divided 7859.6 proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 6417.18 1.22477
Subtracted 11864 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] 13241.4 1377.4
249 Divided 7859.59 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 6417.18 1.22477
Subtracted 5782.08 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 4405.4 1376.68
250 Divided 7859.6 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 6417.18 1.22477
Subtracted 5939.91 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] 4578.09 1361.82

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/