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 18670 to 18719 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2334 synapsin ii. [swissprot;acc:q92777] Squared Divided 28264.4 30386.4 1.07508
transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] Rooted Subtracted 66.412 67.5994 1.1874
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Ranked Divided 229.258 230.294 1.00452
2335 adaptor-associated kinase 1. [refseq;acc:nm_014911] Squared Subtracted 25184.6 26642.9 1458.3
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] Rooted 59.0309 60.2133 1.1824
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Measured 5265.95 5492.28 226.33
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Rooted Divided 82.0144 80.5316 1.01841
microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Measured 5123.89 5350.78 1.04428
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Squared 28264.4 30386.4 1.07508
serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Ranked Subtracted 217.057 218.03 0.973
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Divided 229.258 230.294 1.00452
2336 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Squared Subtracted 25184.4 26642.7 1458.3
bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] Measured 5254.55 5480.56 226.01
coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] Rooted Divided 76.7325 75.3464 1.0184
dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Subtracted 59.0309 60.2133 1.1824
neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Ranked Divided 229.258 230.294 1.00452
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Squared 28264.4 30386.4 1.07508
serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] Ranked Subtracted 217.057 218.03 0.973
uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Measured Divided 5123.89 5350.78 1.04428
2337 40s ribosomal protein s29. [swissprot;acc:p30054] Subtracted 3582.57 3357.6 224.97
arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Rooted 66.4972 67.6694 1.1722
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] Measured Divided 5123.89 5350.78 1.04428
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Squared Subtracted 25184.6 26642.9 1458.3
glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] Ranked 217.057 218.03 0.973
hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] Squared Divided 28264.4 30386.4 1.07508
homeobox protein dlx-2. [swissprot;acc:q07687] Ranked 229.258 230.294 1.00452
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Rooted 81.987 80.5061 1.01839
2338 60s ribosomal protein l32. [swissprot;acc:p02433] Measured Subtracted 3618.02 3394.29 223.73
acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] Ranked 191.571 192.544 0.973
bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Measured Divided 5123.89 5350.78 1.04428
creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Rooted 75.1308 76.5124 1.01839
homeobox protein dlx-5. [swissprot;acc:p56178] Ranked 229.258 230.294 1.00452
protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] Rooted Subtracted 62.1662 60.9991 1.1671
rho-gtpase activating protein 10. [refseq;acc:nm_020824] Squared 25184.6 26642.9 1458.3
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Divided 28264.4 30386.4 1.07508
2339 creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277] Rooted 75.1757 76.5526 1.01832
delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] Squared 28264.4 30386.4 1.07508
fetal brain protein 239 (239fb). [swissprot;acc:q15777] Ranked 229.258 230.294 1.00452
homeobox protein otx2. [swissprot;acc:p32243] Measured Subtracted 5682 5905.08 223.08
phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Divided 5123.89 5350.78 1.04428
rho interacting protein 3. [refseq;acc:nm_015134] Rooted Subtracted 62.167 61.0002 1.1668
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Squared 25184.4 26642.7 1458.3
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Ranked 209.326 208.357 0.969
2340 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Squared Divided 28264.4 30386.4 1.07508
alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] Measured 5607.81 5855.72 1.04421
arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] Rooted Subtracted 66.5228 67.6894 1.1666
growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] Squared 25184.6 26642.9 1458.3
homeobox protein dlx-3. [swissprot;acc:o60479] Ranked Divided 229.258 230.294 1.00452
homeobox protein otx1. [swissprot;acc:p32242] Measured Subtracted 5691.1 5913.92 222.82
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 0.965

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/