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 12264 to 12313 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1533 vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Rooted Subtracted 63.2569 65.5867 2.3298
1534 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 63.0853 65.4141 2.3288
adp-ribosylation factor-like protein 3. [swissprot;acc:p36405] Measured Divided 5916.05 6350.53 1.07344
glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947] Rooted 63.304 65.6156 1.03652
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Ranked 228.419 232.376 1.01732
mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [swissprot;acc:p28482] Squared 28603.7 31846.4 1.11337
phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] Measured Subtracted 6157.13 6591.53 434.4
trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] Squared 22766.5 25361.9 2595.4
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Ranked 213.259 209.524 3.735
1535 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] 225.159 221.424
aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] Measured 5945.96 6380.28 434.32
enigma protein; lim domain protein. [refseq;acc:nm_005451] Rooted 61.1844 63.5127 2.3283
heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Ranked Divided 228.419 232.376 1.01732
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357] Rooted 63.304 65.6156 1.03652
ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] Squared 25840.7 28767.8 1.11327
unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] Measured 5916.05 6350.53 1.07344
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Squared Subtracted 27944.1 30539.3 2595.2
1536 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556] Measured Divided 5916.05 6350.53 1.07344
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Ranked Subtracted 216.762 213.031 3.731
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Measured 5984.88 6419.11 434.23
epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Squared Divided 31846.9 35454 1.11326
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Rooted Subtracted 61.1844 63.5127 2.3283
fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] Ranked Divided 228.419 232.376 1.01732
putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Squared Subtracted 24853.2 27447.8 2594.6
ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [swissprot;acc:q9uk32] Rooted Divided 63.3039 65.6156 1.03652
1537 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] Squared 26432.8 29419.4 1.11299
cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] Ranked Subtracted 217.025 213.304 3.721
delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Rooted 64.0988 66.426 2.3272
evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] Measured Divided 6184.27 6637.44 1.07328
mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Squared Subtracted 21786.2 24380.3 2594.1
p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Measured 5696.65 6130.26 433.61
ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [swissprot;acc:q15349] Rooted Divided 63.3039 65.6156 1.03652
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Ranked 228.419 232.376 1.01732
1538 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] Squared 30653.9 34111.1 1.11278
brachyury protein (t protein). [swissprot;acc:o15178] Measured Subtracted 6179.59 6613.15 433.56
calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7] Rooted Divided 63.304 65.6156 1.03652
elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] Ranked 228.419 232.376 1.01732
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Squared Subtracted 21782 24375.4 2593.4
myb-related protein b (b-myb). [swissprot;acc:p10244] Ranked 222.541 218.823 3.718
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Rooted 63.8741 66.193 2.3189
tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Measured Divided 5870.72 6300.83 1.07326
1539 26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998] 5783.97 6207.5 1.07322
calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [swissprot;acc:q13554] Rooted 63.304 65.6156 1.03652
colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] Squared 29291.1 32591.4 1.11267
myb-related protein a (a-myb). [swissprot;acc:p10243] Ranked Subtracted 222.512 218.802 3.71
phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] Rooted 63.8741 66.1929 2.3188
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 2592.6
rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] Ranked Divided 228.419 232.376 1.01732
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Measured Subtracted 6179.59 6613.15 433.56
1540 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] Ranked 217.769 221.474 3.705

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/