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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4608 to 4657 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2304 signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] Subtracted 5514.85 5755.17 240.32
2305 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] Divided 6946.82 7263.87 1.04564
signal transducer and activator of transcription 4. [swissprot;acc:q14765] Subtracted 5514.83 5755.14 240.31
2306 dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Divided 3619.07 3461.21 1.04561
signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] Subtracted 5514.81 5755.1 240.29
2307 fas apoptotic inhibitory molecule. [refseq;acc:nm_018147] Divided 5666.91 5923.48 1.04528
germ cell-less. [refseq;acc:nm_022471] Subtracted 7764.92 8003.67 238.75
2308 60s ribosomal protein l7. [swissprot;acc:p18124] Divided 3976.92 3804.85 1.04522
pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] Subtracted 7765.3 8004 238.7
2309 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] Divided 6960.96 7273.7 1.04493
pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] Subtracted 7765.3 8004 238.7
2310 hyporthetical protein mgc27169. [refseq;acc:nm_176782]
lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Divided 6960.96 7273.7 1.04493
2311 homeobox protein meis1. [swissprot;acc:o00470] Subtracted 7765.3 8004 238.7
solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] Divided 6961.19 7273.93 1.04493
2312 homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] Subtracted 7765.3 8004 238.7
very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975] Divided 6960.26 7273.01 1.04493
2313 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] Subtracted 7765.3 8004 238.7
disrupter of silencing 10. [refseq;acc:nm_020368] Divided 6960.96 7273.7 1.04493
2314 pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] Subtracted 7765.3 8004 238.7
very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] Divided 6960.99 7273.72 1.04493
2315 pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] Subtracted 7765.3 8004 238.7
solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] Divided 6961.11 7273.85 1.04493
2316 homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] Subtracted 7765.3 8004 238.7
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] Divided 6960.74 7273.48 1.04493
2317 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] Subtracted 5150.31 5388.05 237.74
solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] Divided 6961.44 7274.17 1.04492
2318 block 23. [sptrembl;acc:q8nhw5] Subtracted 5150.14 5387.84 237.7
ubiquitin. [swissprot;acc:p02248] Divided 7484.98 7821.11 1.04491
2319 hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] Subtracted 4561.75 4799.24 237.49
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Divided 6362.48 6647.42 1.04478
2320 similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Subtracted 5148.88 5386.34 237.46
t54 protein. [swissprot;acc:q92917] Divided 6362.48 6647.42 1.04478
2321 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 3496.21 3652.28 1.04464
wd repeat domain 26. [refseq;acc:nm_025160] Subtracted 6423.46 6655.9 232.44
2322 atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] 5262.6 5492.58 229.98
mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] Divided 6773.67 7075.51 1.04456
2323 mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797]
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Subtracted 6123.47 6351.84 228.37
2324 cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833] Divided 6773.67 7075.51 1.04456
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Subtracted 5123.89 5350.78 226.89
2325 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]
mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] Divided 6773.67 7075.51 1.04456
2326 histone deacetylase 11 (hd11). [swissprot;acc:q96db2]
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] Subtracted 5123.89 5350.78 226.89
2327 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] Divided 6773.67 7075.51 1.04456
2328 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Subtracted 5123.89 5350.78 226.89
ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6] Divided 6773.67 7075.51 1.04456
2329 hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232]

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/