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 3480 to 3529 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
870 transcription factor btf3 homolog 3. [swissprot;acc:q13892] Ranked 211.908 203.832 1.03962
871 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 110.2 114.552 1.03949
protein bap28. [swissprot;acc:q9h583] Measured 3956.25 4364.25 1.10313
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Squared 20281 23528.5 1.16013
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Rooted 84.6378 89.8201 1.06123
872 epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Measured 6781.05 7480.15 1.1031
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Squared 18650.4 21632 1.15987
heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] Ranked 224.413 233.272 1.03948
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] Rooted 84.6378 89.8201 1.06123
873 myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] Squared 18650.4 21632 1.15987
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Measured 4749.52 5237.77 1.1028
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] Rooted 84.6378 89.8201 1.06123
u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] Ranked 224.413 233.272 1.03948
874 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 212.002 203.954 1.03946
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Measured 9921.43 10941.2 1.10278
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Rooted 84.6378 89.8201 1.06123
myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] Squared 18650.4 21632 1.15987
875 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Ranked 212.002 203.954 1.03946
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] Squared 18650.4 21632 1.15987
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Rooted 84.6378 89.8201 1.06123
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Measured 10263.8 11318.6 1.10277
876 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Ranked 212.002 203.954 1.03946
myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] Squared 18650.4 21632 1.15987
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Rooted 84.6378 89.8201 1.06123
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Measured 5644.68 6223.23 1.10249
877 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Ranked 212.002 203.954 1.03946
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Measured 5797.88 6391.75 1.10243
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Squared 18650.4 21632 1.15987
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Rooted 84.6378 89.8201 1.06123
878 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Ranked 212.002 203.954 1.03946
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Measured 5797.88 6391.75 1.10243
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Rooted 84.6378 89.8201 1.06123
triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Squared 23242.1 26955.1 1.15975
879 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Ranked 212.002 203.954 1.03946
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] Squared 23242.1 26955.1 1.15975
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Rooted 84.6378 89.8201 1.06123
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Measured 5797.88 6391.75 1.10243
880 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Ranked 212.002 203.954 1.03946
lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Squared 23242.1 26955.1 1.15975
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Rooted 84.6378 89.8201 1.06123
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Measured 5166.04 5694.55 1.1023
881 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 5912.84 6517.69 1.10229
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Ranked 227.604 219.001 1.03928
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] Rooted 84.6378 89.8201 1.06123
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Squared 23242.1 26955.1 1.15975
882 n-myc proto-oncogene protein. [swissprot;acc:p04198] Ranked 227.601 219.008 1.03924
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Rooted 84.6378 89.8201 1.06123
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Squared 23242.1 26955.1 1.15975
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Measured 5912.84 6517.69 1.10229
883 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]

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/