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 4591 to 4640 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1148 hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Measured 6281.21 6837.61 1.08858
ubiquitin. [swissprot;acc:p02248] Ranked 209.061 203.518 1.02724
1149 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] Rooted 61.5672 64.5415 1.04831
bystin. [swissprot;acc:q13895] Ranked 239.505 233.185 1.0271
transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Measured 6280.74 6837.01 1.08857
ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] Squared 28101.6 32027.6 1.13971
1150 kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679]
mstp028 protein. [refseq;acc:nm_031954] Measured 5838.87 6355.06 1.08841
sorting nexin 1. [swissprot;acc:q13596] Ranked 209.868 215.522 1.02694
translation initiation factor if-2. [swissprot;acc:o60841] Rooted 62.5721 65.592 1.04826
1151 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] Measured 5322.74 5793.15 1.08838
metaxin 1. [swissprot;acc:q13505] Ranked 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
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534] Squared 28101.6 32027.6 1.13971
1152 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Measured 5322.74 5793.15 1.08838
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 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
tata element modulatory factor (tmf). [swissprot;acc:p82094] Rooted 59.9298 62.8125 1.0481
1153 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] Squared 26906.6 30660.6 1.13952
epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] Ranked 221.93 216.146 1.02676
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 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
inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] Ranked 224.307 230.242 1.02646
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Rooted 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
1155 ammecr1 protein. [refseq;acc:nm_015365] Rooted 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
transducin-like enhancer protein 4. [swissprot;acc:q04727] Measured 6270.67 6823.73 1.0882
1156 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Squared 26905.4 30657.2 1.13944
aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] Ranked 224.307 230.242 1.02646
mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Rooted 59.9298 62.8125 1.0481
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Measured 5840.77 6355.89 1.08819
1157 ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Ranked 224.307 230.242 1.02646
dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Squared 21673.6 24695.2 1.13941
dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] Rooted 52.7311 50.3121 1.04808
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Measured 5418.33 5895.2 1.08801
1158 atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] Rooted 63.2606 66.301 1.04806
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Measured 5489.18 5972.09 1.08797
dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Squared 21674.5 24695.2 1.13937
epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] Ranked 221.877 216.167 1.02641
1159 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Squared 25705.5 29282.6 1.13916
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Rooted 66.427 69.5971 1.04772
kccr13l. [refseq;acc:nm_139179] Measured 5538.8 6025.51 1.08787
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Ranked 170.28 165.898 1.02641
1160 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 208.55 214.041 1.02633
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Squared 25705.5 29282.6 1.13916
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Rooted 61.4957 64.429 1.0477
dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609] Measured 5538.8 6025.51 1.08787

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/