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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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 13264 to 13313 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1156 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Measured Subtracted 5826.29 6335.93 509.64
1157 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 5826.32 6335.95 509.63
ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Ranked Divided 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
mesoderm induction early response 1. [refseq;acc:nm_020948] Squared Subtracted 29813.9 32974.4 3160.5
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Measured Divided 5418.33 5895.2 1.08801
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Rooted Subtracted 60.5003 63.437 2.9367
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Ranked 220.742 215.237 5.505
1158 atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] Rooted Divided 63.2606 66.301 1.04806
calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] Subtracted 61.4957 64.4292 2.9335
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Measured Divided 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
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Measured Subtracted 5973.95 6483.32 509.37
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Squared 29813.9 32974.4 3160.5
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Ranked 220.742 215.237 5.505
1159 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] Squared 17618.8 20776.8 3158
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Divided 25705.5 29282.6 1.13916
caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] Rooted Subtracted 55.3631 58.2965 2.9334
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Divided 66.427 69.5971 1.04772
eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Measured Subtracted 3975.77 4485.05 509.28
kccr13l. [refseq;acc:nm_139179] Divided 5538.8 6025.51 1.08787
lbp-9. [refseq;acc:nm_014553] Ranked Subtracted 220.742 215.237 5.505
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Divided 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
apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] Rooted Subtracted 55.3631 58.2965 2.9334
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Squared Divided 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
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Ranked Subtracted 220.742 215.237 5.505
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Measured 3975.77 4485.05 509.28
wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] Squared 28992.5 32145.6 3153.1
1161 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Ranked 218.402 212.904 5.498
autoantigen ngp-1. [swissprot;acc:q13823] Measured 3766.14 4274.79 508.65
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Squared Divided 25705.2 29282.3 1.13916
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Rooted Subtracted 61.4957 64.429 2.9333
kappa b-ras 1. [refseq;acc:nm_020345] Ranked Divided 220.758 215.097 1.02632
n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] Measured 5315.76 5782.63 1.08783
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Squared Subtracted 17550.2 20701.1 3150.9
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] Rooted Divided 61.4957 64.429 1.0477
1162 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] Squared Subtracted 58201.3 55052 3149.3
calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] Rooted Divided 61.4956 64.4289 1.0477
chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] Measured Subtracted 5799.35 6305.95 506.6
i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] Ranked Divided 220.758 215.097 1.02632
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Measured 5832.13 6343.59 1.0877
rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] Squared 25712.1 29288.6 1.1391
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Ranked Subtracted 218.402 212.904 5.498
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] Rooted 61.4957 64.429 2.9333
1163 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] Measured 5799.35 6305.95 506.6

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/