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 11214 to 11263 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2302 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] Rooted 59.4004 60.5463 1.01929
hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] Ranked 191.567 192.542 1.00509
transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9] Squared 35770.9 38515.2 1.07672
2303 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] Ranked 191.567 192.542 1.00509
hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] Measured 6946.6 7263.68 1.04565
putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] Rooted 59.4004 60.5463 1.01929
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Squared 35770.9 38515.2 1.07672
2304 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] Measured 6946.38 7263.48 1.04565
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] Squared 35770.9 38515.2 1.07672
hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] Ranked 191.567 192.542 1.00509
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Rooted 58.8299 59.9634 1.01927
2305 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] 59.0186 60.1552 1.01926
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] Measured 6946.82 7263.87 1.04564
delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] Ranked 217.392 218.498 1.00509
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Squared 35770.9 38515.2 1.07672
2306 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] Ranked 191.571 192.544 1.00508
brain protein 16. [refseq;acc:nm_016458] Rooted 62.158 63.3479 1.01914
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Measured 3619.07 3461.21 1.04561
transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] Squared 35770.9 38515.2 1.07672
2307 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] Ranked 215.554 214.467 1.00507
fas apoptotic inhibitory molecule. [refseq;acc:nm_018147] Measured 5666.91 5923.48 1.04528
nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494] Squared 35770.9 38515.2 1.07672
rho interacting protein 3. [refseq;acc:nm_015134] Rooted 62.167 61.0002 1.01913
2308 60s ribosomal protein l7. [swissprot;acc:p18124] Measured 3976.92 3804.85 1.04522
nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] Squared 35770.9 38515.2 1.07672
protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] Ranked 215.543 214.459 1.00505
protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] Rooted 62.1662 60.9991 1.01913
2309 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Ranked 215.542 214.459 1.00505
delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062] Measured 6960.96 7273.7 1.04493
glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211] Squared 30076.7 32382.8 1.07667
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Rooted 70.5239 71.8706 1.0191
2310 dc11 protein. [refseq;acc:nm_020186]
deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] Squared 15947.3 17167.1 1.07649
lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Measured 6960.96 7273.7 1.04493
ubiquitin. [swissprot;acc:p02248] Ranked 216.617 215.529 1.00505
2311 amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] Rooted 70.5239 71.8706 1.0191
camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] Ranked 215.542 214.459 1.00505
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Squared 15947.3 17167.1 1.07649
solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] Measured 6961.19 7273.93 1.04493
2312 5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] Rooted 70.5239 71.8706 1.0191
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] Ranked 215.542 214.459 1.00505
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Squared 15947.3 17167.1 1.07649
very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975] Measured 6960.26 7273.01 1.04493
2313 camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] Ranked 215.529 214.449 1.00504
disrupter of silencing 10. [refseq;acc:nm_020368] Measured 6960.96 7273.7 1.04493
map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] Squared 15947.3 17167.1 1.07649
ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Rooted 70.5239 71.8706 1.0191
2314 meiotic recombination protein spo11. [swissprot;acc:q9y5k1] Squared 15947.3 17167.1 1.07649
ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314] Rooted 70.5239 71.8706 1.0191
ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Ranked 194.743 195.708 1.00496

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/