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 4658 to 4707 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1165 importin 4. [refseq;acc:nm_024658] Squared 24917.7 28380.8 1.13898
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Measured 6604.44 7183.07 1.08761
transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Ranked 219.401 213.785 1.02627
1166 proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Squared 23379.3 26625.2 1.13884
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Rooted 95.094 90.7685 1.04765
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Measured 6606.3 7185.01 1.0876
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Ranked 219.374 213.759 1.02627
1167 homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] 219.399 213.784 1.02626
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Squared 23165.9 26375.7 1.13856
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Measured 6607.68 7186.45 1.08759
suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] Rooted 62.8958 65.8878 1.04757
1168 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Ranked 219.399 213.784 1.02626
delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] Squared 23165.9 26375.7 1.13856
glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] Rooted 62.8958 65.8878 1.04757
mitotic checkpoint protein bub3. [swissprot;acc:o43684] Measured 5470.44 5949.49 1.08757
1169 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Ranked 219.399 213.784 1.02626
asc-1 complex subunit p100. [refseq;acc:nm_032204] Rooted 62.8958 65.8878 1.04757
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Squared 19625.9 22341.9 1.13839
zinc finger protein 207. [swissprot;acc:o43670] Measured 5470.44 5949.49 1.08757
1170 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Ranked 219.399 213.784 1.02626
fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] Rooted 62.8958 65.8878 1.04757
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Squared 20923.6 23813.2 1.1381
ubiquitin-like protein smt3a. [swissprot;acc:p55854] Measured 5826.34 6335.98 1.08747
1171 40s ribosomal protein s28. [swissprot;acc:p25112] Rooted 70.4215 73.7627 1.04745
hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Ranked 219.399 213.784 1.02626
microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Squared 20923.6 23813.2 1.1381
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Measured 5826.29 6335.93 1.08747
1172 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 5826.32 6335.95
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Rooted 63.4397 66.4483 1.04742
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Ranked 219.375 213.767 1.02623
uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Squared 20923.6 23813.2 1.1381
1173 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] Ranked 229.243 235.246 1.02619
chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] Measured 5799.35 6305.95 1.08735
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] Squared 20923.6 23813.2 1.1381
cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Rooted 60.9172 63.8009 1.04734
1174 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48]
bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Squared 20923.6 23813.2 1.1381
cda11 protein. [refseq;acc:nm_032026] Measured 5874.11 6387.23 1.08735
coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] Ranked 187.964 192.849 1.02599
1175 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] Measured 5799.35 6305.95 1.08735
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Rooted 61.2655 64.1634 1.0473
phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Squared 20923.6 23813.2 1.1381
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Ranked 218.186 212.672 1.02593
1176 aarf domain containing kinase 4. [refseq;acc:nm_024876] Measured 5799.35 6305.95 1.08735
ring finger protein 44. [refseq;acc:nm_014901] Rooted 61.2655 64.1634 1.0473
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Ranked 218.186 212.672 1.02593
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Squared 22201.6 25263.1 1.1379
1177 aarf domain containing kinase 1. [refseq;acc:nm_020421] Measured 5799.35 6305.95 1.08735
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] Ranked 218.186 212.672 1.02593
mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Squared 22813.2 25958.3 1.13786

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/