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 13214 to 13263 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1150 sorting nexin 1. [swissprot;acc:q13596] Ranked Divided 209.868 215.522 1.02694
translation initiation factor if-2. [swissprot;acc:o60841] Rooted 62.5721 65.592 1.04826
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Ranked Subtracted 218.186 212.672 5.514
1151 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] Rooted 61.5672 64.5415 2.9743
60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] Squared 23538.3 26712.4 3174.1
alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] Measured Divided 5322.74 5793.15 1.08838
dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Subtracted 5998.58 6509.65 511.07
metaxin 1. [swissprot;acc:q13505] Ranked Divided 199.552 204.925 1.02693
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] Rooted 58.3991 61.2163 1.04824
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Ranked Subtracted 218.186 212.672 5.514
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534] Squared Divided 28101.6 32027.6 1.13971
1152 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Measured Subtracted 5998.69 6509.74 511.05
beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Divided 5322.74 5793.15 1.08838
bystin. [swissprot;acc:q13895] Rooted Subtracted 53.1515 56.1209 2.9694
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Squared Divided 21669.8 24695.2 1.13961
epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Ranked 221.939 216.143 1.02682
golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] Subtracted 218.186 212.672 5.514
tata element modulatory factor (tmf). [swissprot;acc:p82094] Rooted Divided 59.9298 62.8125 1.0481
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] Squared Subtracted 40276.1 37105 3171.1
1153 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] Divided 26906.6 30660.6 1.13952
delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Ranked Subtracted 218.186 212.672 5.514
epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] Divided 221.93 216.146 1.02676
meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] Measured Subtracted 5913.73 6423.98 510.25
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Rooted 56.1832 53.2244 2.9588
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Squared 26952.5 30122.8 3170.3
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Rooted Divided 59.9298 62.8125 1.0481
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Measured 5840.01 6355.56 1.08828
1154 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] Squared 26906.6 30660.6 1.13952
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Rooted Subtracted 56.1854 53.2272 2.9582
cellular modulator of immune recognition. [refseq;acc:nm_145021] Ranked 218.186 212.672 5.514
inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] Divided 224.307 230.242 1.02646
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Squared Subtracted 26952.5 30122.8 3170.3
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Rooted Divided 59.9298 62.8125 1.0481
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Measured 5840.65 6355.84 1.08821
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Subtracted 6004.54 6514.24 509.7
1155 ammecr1 protein. [refseq;acc:nm_015365] Rooted Divided 59.9298 62.8125 1.0481
dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Squared 21672.8 24695.2 1.13946
inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] Ranked 224.307 230.242 1.02646
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Squared Subtracted 26952.5 30122.8 3170.3
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Rooted 66.4107 69.3664 2.9557
transducin-like enhancer protein 4. [swissprot;acc:q04727] Measured Divided 6270.67 6823.73 1.0882
ubiquitin-like protein smt3a. [swissprot;acc:p55854] Subtracted 5826.34 6335.98 509.64
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Ranked 218.186 212.672 5.514
1156 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Squared Divided 26905.4 30657.2 1.13944
aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] Ranked 224.307 230.242 1.02646
cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] Squared Subtracted 22465.5 25633.4 3167.9
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Ranked 218.186 212.672 5.514
mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Rooted Divided 59.9298 62.8125 1.0481
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Measured 5840.77 6355.89 1.08819
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Rooted Subtracted 64.9834 67.9275 2.9441

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/