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 1180 to 1229 of 3228 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
green
network_comparison
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] 4392.63 4776.19 1.08732
1181 protocadherin 15 precursor. [swissprot;acc:q96qu1]
1182 solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415]
1183 lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]
1184 zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]
1185 suppressor of fused. [refseq;acc:nm_016169]
1186 zinc finger protein gli3. [swissprot;acc:p10071]
1187 limb region 1 protein; limb region 1. [refseq;acc:nm_022458]
1188 gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142]
1189 zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]
1190 mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] 6599.84 7174.29 1.08704
1191 probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11]
1192 tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226]
1193 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] 5464.9 5940.16 1.08697
1194 t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] 8425.35 7751.57 1.08692
1195 similar to trna synthetase class ii. [refseq;acc:nm_152268] 5439.56 5911.24 1.08671
1196 kappa b-ras 1. [refseq;acc:nm_020345] 5721.19 6217.2 1.0867
1197 i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595]
1198 snare associated protein snapin. [refseq;acc:nm_012437]
1199 serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] 5449.48 5921.77 1.08667
1200 xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] 5950.27 6465.72 1.08663
1201 thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] 6042.31 6565.03 1.08651
1202 porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] 4913.07 5337.95 1.08648
1203 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] 4322.65 4696.04 1.08638
1204 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] 5946.33 6459.79 1.08635
1205 glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
1206 asc-1 complex subunit p100. [refseq;acc:nm_032204]
1207 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]
1208 meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] 5913.73 6423.98 1.08628
1209 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 5420.87 5887.53 1.08609
1210 trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] 6410.73 6962.22 1.08603
1211 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
1212 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 4077.89 4428.28 1.08592
1213 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 5890.62 6396.53 1.08588
1214 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] 6001.16 6515.9 1.08577
1215 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 1.08575
1216 fibulin-2 precursor. [swissprot;acc:p98095] 8670.59 9412.9 1.08561
1217 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] 6021.21 6536.45 1.08557
1218 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] 5736 6226.52 1.08552
1219 tcd37 homolog; prune. [refseq;acc:nm_021222] 5735.95 6226.46
1220 cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] 5735.65 6226.13 1.08551
1221 cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] 5736.34 6226.88
1222 cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] 5735.74 6226.23
1223 transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 6011.44 6524.55 1.08536
1224 splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] 4331.35 4700.91 1.08532
1225 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 5546.5 6019.57 1.08529
1226 tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 5997.24 6508.62 1.08527
1227 pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] 5973.95 6483.32
1228 dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] 5998.58 6509.65 1.0852
1229 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 5998.69 6509.74 1.08519

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/