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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3458 to 3507 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
865 Ranked transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 211.961 203.814 1.03997
Squared sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] 24242.8 28127.6 1.16025
Rooted asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] 62.7551 66.6474 1.06202
866 Measured ring finger protein 38. [refseq;acc:nm_022781] 5595.65 6173.23 1.10322
Ranked signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] 221.306 212.806 1.03994
Squared atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] 24242.8 28127.6 1.16025
Rooted probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] 51.8306 55.0247 1.06163
867 Measured phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] 5595.65 6173.23 1.10322
Ranked 40s ribosomal protein s3a. [swissprot;acc:p49241] 225.689 234.674 1.03981
Squared phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] 24242.8 28127.6 1.16025
Rooted mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] 61.668 65.4526 1.06137
868 Measured sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] 5595.65 6173.23 1.10322
Ranked diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] 233.298 242.571 1.03975
Squared keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 31099.4 36082.4 1.16023
Rooted mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 61.668 65.4526 1.06137
869 Measured atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] 5595.65 6173.23 1.10322
Ranked exocyst complex component sec8. [swissprot;acc:q96a65] 217.762 209.449 1.03969
Squared segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 20273.1 23521.2 1.16022
Rooted nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] 61.668 65.4526 1.06137
870 Measured phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] 5595.65 6173.23 1.10322
Ranked transcription factor btf3 homolog 3. [swissprot;acc:q13892] 211.908 203.832 1.03962
Squared signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 21086.3 24464.1 1.16019
Rooted 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] 84.6378 89.8201 1.06123
871 Measured protein bap28. [swissprot;acc:q9h583] 3956.25 4364.25 1.10313
Ranked cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 110.2 114.552 1.03949
Squared segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 20281 23528.5 1.16013
Rooted sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 84.6378 89.8201 1.06123
872 Measured epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] 6781.05 7480.15 1.1031
Ranked heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] 224.413 233.272 1.03948
Squared ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] 18650.4 21632 1.15987
Rooted 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] 84.6378 89.8201 1.06123
873 Measured programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] 4749.52 5237.77 1.1028
Ranked u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] 224.413 233.272 1.03948
Squared myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] 18650.4 21632 1.15987
Rooted 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] 84.6378 89.8201 1.06123
874 Measured ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 9921.43 10941.2 1.10278
Ranked 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 212.002 203.954 1.03946
Squared myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] 18650.4 21632 1.15987
Rooted map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] 84.6378 89.8201 1.06123
875 Measured steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] 10263.8 11318.6 1.10277
Ranked 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 212.002 203.954 1.03946
Squared nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380] 18650.4 21632 1.15987
Rooted neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] 84.6378 89.8201 1.06123
876 Measured peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 5644.68 6223.23 1.10249
Ranked 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 212.002 203.954 1.03946
Squared myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] 18650.4 21632 1.15987
Rooted nitrogen fixation cluster-like. [refseq;acc:nm_014301] 84.6378 89.8201 1.06123
877 Measured mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] 5797.88 6391.75 1.10243
Ranked 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 212.002 203.954 1.03946
Squared myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] 18650.4 21632 1.15987

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/