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 2373 to 2422 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
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
1188 gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142]
probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] Subtracted 5417.07 5917.79 500.72
1189 nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] 5869.24 6367.8 498.56
zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070] Divided 4392.63 4776.19 1.08732
1190 mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] 6599.84 7174.29 1.08704
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Subtracted 4982.81 5480.91 498.1
1191 prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Divided 6599.84 7174.29 1.08704
1192 immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Subtracted 5364.32 5862.09 497.77
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Divided 6599.84 7174.29 1.08704
1193 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] 5464.9 5940.16 1.08697
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Subtracted 6322.75 6820.5 497.75
1194 nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Divided 8425.35 7751.57 1.08692
1195 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Subtracted 6110.09 6607.81 497.72
similar to trna synthetase class ii. [refseq;acc:nm_152268] Divided 5439.56 5911.24 1.08671
1196 kappa b-ras 1. [refseq;acc:nm_020345] 5721.19 6217.2 1.0867
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Subtracted 7659.42 8156.79 497.37
1197 i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] Divided 5721.19 6217.2 1.0867
tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Subtracted 5873.56 6370.31 496.75
1198 snare associated protein snapin. [refseq;acc:nm_012437] Divided 5721.19 6217.2 1.0867
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Subtracted 5873.56 6370.31 496.75
1199 peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] 5489.99 5986.63 496.64
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Divided 5449.48 5921.77 1.08667
1200 phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Subtracted 5489.99 5986.63 496.64
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] Divided 5950.27 6465.72 1.08663
1201 proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] Subtracted 6523.17 7019.44 496.27
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Divided 6042.31 6565.03 1.08651
1202 kappa b-ras 1. [refseq;acc:nm_020345] Subtracted 5721.19 6217.2 496.01
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Divided 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
i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] Subtracted 5721.19 6217.2 496.01
1204 snare associated protein snapin. [refseq;acc:nm_012437]
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] Divided 5946.33 6459.79 1.08635
1205 glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Subtracted 5462.88 5958.12 495.24
1206 asc-1 complex subunit p100. [refseq;acc:nm_032204] Divided 5946.33 6459.79 1.08635
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Subtracted 5460.49 5954.62 494.13
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] Divided 5946.33 6459.79 1.08635
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Subtracted 6105.93 6599.41 493.48
1208 meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] Divided 5913.73 6423.98 1.08628
orphan nuclear receptor tr2. [swissprot;acc:p13056] Subtracted 6105.69 6599.06 493.37
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] Divided 5420.87 5887.53 1.08609
dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Subtracted 5147.9 5641.25 493.35
1210 mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] 6051.23 6544.17 492.94
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] Divided 6410.73 6962.22 1.08603
1211 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Subtracted 5807.83 6300.47 492.64

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/