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 7362 to 7411 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1841 presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Ranked 212.455 210.113 1.01115
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Squared 24032.2 26345.1 1.09624
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Rooted 89.4611 86.8531 1.03003
1842 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Measured 3591.95 3375.34 1.06417
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Rooted 61.38 63.2221 1.03001
gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] Ranked 212.455 210.113 1.01115
glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] Squared 24032.2 26345.1 1.09624
1843 glutamyl trna synthetase. [sptrembl;acc:o14563]
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Measured 3591.95 3375.34 1.06417
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Ranked 212.455 210.113 1.01115
ubiquitin-like protein smt3a. [swissprot;acc:p55854] Rooted 63.5262 65.4316 1.02999
1844 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Measured 3591.95 3375.34 1.06417
paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] Ranked 214.773 212.417 1.01109
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Squared 33450.5 30514.3 1.09622
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Rooted 63.5261 65.4314 1.02999
1845 abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] Ranked 217.077 214.702 1.01106
acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Rooted 63.5262 65.4315 1.02999
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Measured 3591.95 3375.34 1.06417
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Squared 13266.3 14540.4 1.09604
1846 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Rooted 52.887 54.4715 1.02996
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Measured 3591.95 3375.34 1.06417
protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Squared 27001 29593.6 1.09602
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Ranked 217.066 214.698 1.01103
1847 brain protein 16. [refseq;acc:nm_016458] 216.811 219.195 1.011
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Measured 6215.55 6613.46 1.06402
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Squared 26990.9 29579.6 1.09591
transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] Rooted 68.9584 71.0209 1.02991
1848 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] 64.27 66.1875 1.02984
bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] Ranked 218.441 216.064 1.011
heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900] Measured 5746.06 6113.79 1.064
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Squared 30518.9 33445.2 1.09588
1849 apical-like protein (apxl protein). [swissprot;acc:q13796] 30517.3 33442.4 1.09585
arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Measured 6267.93 6668.72 1.06394
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Ranked 218.445 216.074 1.01097
ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792] Rooted 61.8519 63.6966 1.02982
1850 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] Ranked 215.931 213.587 1.01097
dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] Squared 26167 28674.3 1.09582
protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [swissprot;acc:q9ulu4] Measured 6158.6 6551.94 1.06387
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Rooted 65.0281 66.9647 1.02978
1851 adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326] Measured 6156.28 6549.03 1.0638
beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] Squared 26167.1 28674.2 1.09581
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] Ranked 218.448 216.08 1.01096
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted 61.8466 63.6861 1.02974
1852 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Ranked 196.008 198.154 1.01095
arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] Measured 6271.17 6670.97 1.06375
beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] Squared 26167.1 28674.2 1.09581
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Rooted 63.7444 65.6383 1.02971
1853 keratin associated protein 9.2. [refseq;acc:nm_031961] Measured 6076.65 6463.64 1.06368
nitrilase 1. [refseq;acc:nm_005600] Squared 26167.1 28674.2 1.09581
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted 61.8436 63.6804 1.0297

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/