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 4686 to 4735 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1172 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
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Rooted 61.2655 64.1634 1.0473
1178 delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Ranked 218.186 212.672 1.02593
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Measured 4392.63 4776.19 1.08732
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Squared 22813.2 25958.3 1.13786
ring finger protein 38. [refseq;acc:nm_022781] Rooted 61.2655 64.1634 1.0473
1179 cellular modulator of immune recognition. [refseq;acc:nm_145021] Ranked 218.186 212.672 1.02593
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Squared 22813.2 25958.3 1.13786
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] Rooted 61.2655 64.1634 1.0473
solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749] Measured 4392.63 4776.19 1.08732
1180 farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324]
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Squared 22813.2 25958.3 1.13786
sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Rooted 61.2655 64.1634 1.0473
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Ranked 218.186 212.672 1.02593
1181 atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Rooted 61.2655 64.1634 1.0473
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Squared 22813.2 25958.3 1.13786
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Ranked 218.186 212.672 1.02593
protocadherin 15 precursor. [swissprot;acc:q96qu1] Measured 4392.63 4776.19 1.08732
1182 mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Squared 22813.2 25958.3 1.13786
neurocalcin delta. [swissprot;acc:p29554] Ranked 225.104 230.931 1.02589
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Rooted 61.2655 64.1634 1.0473
solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415] Measured 4392.63 4776.19 1.08732
1183 lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]
neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] Ranked 225.103 230.928 1.02588
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Squared 20094.7 22861.9 1.13771
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Rooted 70.4902 73.8211 1.04725
1184 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] Ranked 216.729 222.334 1.02586
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Rooted 64.7687 67.8232 1.04716
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Squared 20094.7 22861.9 1.13771

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/