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 2325 to 2374 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1163 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] Subtracted 5799.35 6305.95 506.6
elks protein. [refseq;acc:nm_015064] Divided 5832.13 6343.59 1.0877
1164 aarf domain containing kinase 4. [refseq;acc:nm_024876] Subtracted 5799.35 6305.95 506.6
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Divided 6600.36 7178.84 1.08764
1165 aarf domain containing kinase 1. [refseq;acc:nm_020421] Subtracted 5799.35 6305.95 506.6
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Divided 6604.44 7183.07 1.08761
1166 exocyst complex component sec8. [swissprot;acc:q96a65] Subtracted 6221.22 6727.77 506.55
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Divided 6606.3 7185.01 1.0876
1167 myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Subtracted 5417.95 5924.41 506.46
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Divided 6607.68 7186.45 1.08759
1168 elongation factor 2 (ef-2). [swissprot;acc:p13639] Subtracted 5494.73 6001.08 506.35
mitotic checkpoint protein bub3. [swissprot;acc:o43684] Divided 5470.44 5949.49 1.08757
1169 metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Subtracted 5494.73 6001.08 506.35
zinc finger protein 207. [swissprot;acc:o43670] Divided 5470.44 5949.49 1.08757
1170 metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Subtracted 5494.73 6001.08 506.35
ubiquitin-like protein smt3a. [swissprot;acc:p55854] Divided 5826.34 6335.98 1.08747
1171 red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Subtracted 4986.58 5492.51 505.93
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Divided 5826.29 6335.93 1.08747
1172 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 5826.32 6335.95
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Subtracted 5890.62 6396.53 505.91
1173 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 5892.05 6397.28 505.23
chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] Divided 5799.35 6305.95 1.08735
1174 cda11 protein. [refseq;acc:nm_032026] 5874.11 6387.23
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Subtracted 4088.63 4593.43 504.8
1175 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] Divided 5799.35 6305.95 1.08735
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Subtracted 4088.63 4593.43 504.8
1176 aarf domain containing kinase 4. [refseq;acc:nm_024876] Divided 5799.35 6305.95 1.08735
myb-related protein b (b-myb). [swissprot;acc:p10244] Subtracted 5418.92 5923.09 504.17
1177 aarf domain containing kinase 1. [refseq;acc:nm_020421] Divided 5799.35 6305.95 1.08735
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Subtracted 5421.93 5926.08 504.15
1178 myb-related protein a (a-myb). [swissprot;acc:p10243] 5419.18 5922.84 503.66
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Divided 4392.63 4776.19 1.08732
1179 fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Subtracted 4019.88 4522.61 502.73
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] Divided 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]
tata element modulatory factor (tmf). [swissprot;acc:p82094] Subtracted 5412.23 5913.4 501.17
1181 protocadherin 15 precursor. [swissprot;acc:q96qu1] Divided 4392.63 4776.19 1.08732
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] Subtracted 5412.23 5913.4 501.17
1182 nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]
solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415] Divided 4392.63 4776.19 1.08732
1183 ammecr1 protein. [refseq;acc:nm_015365] Subtracted 5412.23 5913.4 501.17
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] Divided 4392.63 4776.19 1.08732
1184 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Subtracted 5412.23 5913.4 501.17
zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Divided 4392.63 4776.19 1.08732
1185 peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Subtracted 6522.96 7023.77 500.81
suppressor of fused. [refseq;acc:nm_016169] Divided 4392.63 4776.19 1.08732
1186 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Subtracted 6222.8 6723.54 500.74
zinc finger protein gli3. [swissprot;acc:p10071] Divided 4392.63 4776.19 1.08732
1187 leucyl-trna synthetase. [refseq;acc:nm_020117] Subtracted 5417.06 5917.79 500.73
limb region 1 protein; limb region 1. [refseq;acc:nm_022458] Divided 4392.63 4776.19 1.08732

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/