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 8864 to 8913 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2216 possible global transcription activator snf2l1. [swissprot;acc:p28370] Squared 25245.9 27349.2 1.08331
2217 isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Rooted 62.7032 64.0446 1.02139
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Measured 5910.12 6199.28 1.04893
tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981] Squared 25245.9 27349.2 1.08331
wd-repeat protein 4. [swissprot;acc:p57081] Ranked 221.509 220.108 1.00637
2218 mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] Rooted 65.8854 67.2916 1.02134
myelin p2 protein. [swissprot;acc:p02689] Ranked 221.509 220.108 1.00637
possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531] Squared 25245.9 27349.2 1.08331
wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] Measured 6628.99 6952.04 1.04873
2219 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 5853.67 6136.97 1.0484
kelch-like protein 8. [swissprot;acc:q9p2g9] Ranked 221.509 220.108 1.00637
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] Rooted 65.8854 67.2916 1.02134
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Squared 14191.6 15370.5 1.08307
2220 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Measured 3936.2 3755.33 1.04816
cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833] Rooted 65.8854 67.2916 1.02134
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Squared 14200.2 15379.2 1.08303
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Ranked 221.509 220.108 1.00637
2221 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] Rooted 65.8854 67.2916 1.02134
swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074] Squared 25237.9 27332 1.08297
thrombospondin 3 precursor. [swissprot;acc:p49746] Measured 3936.33 3755.5 1.04815
2222 beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] Ranked 221.509 220.108 1.00637
histone deacetylase 11 (hd11). [swissprot;acc:q96db2] Rooted 65.8854 67.2916 1.02134
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Squared 29345.2 31776.1 1.08284
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Measured 5309.65 5066.82 1.04793
2223 abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] 5864.49 6145.14 1.04786
ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] Rooted 65.8854 67.2916 1.02134
fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Ranked 221.509 220.108 1.00637
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Squared 15953.5 17274.8 1.08282
2224 ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6] Rooted 65.8854 67.2916 1.02134
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Squared 15953.2 17274.4 1.08282
quaking isoform 6. [sptrembl;acc:q9p0x9] Measured 5864.49 6145.14 1.04786
retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] Ranked 221.509 220.108 1.00637
2225 60s ribosomal protein l9. [swissprot;acc:p32969] Measured 3750.99 3580.35 1.04766
cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Squared 15945.8 17266.4 1.08282
hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232] Rooted 65.8854 67.2916 1.02134
indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] Ranked 221.509 220.108 1.00637
2226 cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] 217.955 219.336 1.00634
cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837] Rooted 65.8854 67.2916 1.02134
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Squared 15961.5 17283.3 1.08281
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Measured 3650.78 3484.91 1.0476
2227 cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281] Ranked 217.955 219.336 1.00634
gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Measured 3650.78 3484.91 1.0476
mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [swissprot;acc:o15198] Rooted 65.8854 67.2916 1.02134
presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] Squared 26584 28784.7 1.08278
2228 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Measured 3650.82 3484.97 1.04759
channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] Squared 26586.2 28786.6 1.08276
mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [swissprot;acc:q99717] Rooted 65.8854 67.2916 1.02134
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Ranked 211.81 213.153 1.00634
2229 destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] 217.955 219.336

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/