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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Value Type Rank Gene Network Comparison Type description Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 2375 to 2424 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
red
network_comparison
green
1188 Divided gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142] 4392.63 1.08732 4776.19
Subtracted probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] 5417.07 500.72 5917.79
1189 Divided zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070] 4392.63 1.08732 4776.19
Subtracted nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] 5869.24 498.56 6367.8
1190 Divided mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] 6599.84 1.08704 7174.29
Subtracted prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] 4982.81 498.1 5480.91
1191 Divided probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] 6599.84 1.08704 7174.29
Subtracted prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] 4982.81 498.1 5480.91
1192 Divided tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] 6599.84 1.08704 7174.29
Subtracted immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] 5364.32 497.77 5862.09
1193 Divided putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] 5464.9 1.08697 5940.16
Subtracted sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] 6322.75 497.75 6820.5
1194 Divided t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] 8425.35 1.08692 7751.57
Subtracted nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] 6322.75 497.75 6820.5
1195 Divided similar to trna synthetase class ii. [refseq;acc:nm_152268] 5439.56 1.08671 5911.24
Subtracted protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] 6110.09 497.72 6607.81
1196 Divided kappa b-ras 1. [refseq;acc:nm_020345] 5721.19 1.0867 6217.2
Subtracted 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] 7659.42 497.37 8156.79
1197 Divided i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] 5721.19 1.0867 6217.2
Subtracted tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] 5873.56 496.75 6370.31
1198 Divided snare associated protein snapin. [refseq;acc:nm_012437] 5721.19 1.0867 6217.2
Subtracted sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] 5873.56 496.75 6370.31
1199 Divided serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] 5449.48 1.08667 5921.77
Subtracted peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] 5489.99 496.64 5986.63
1200 Divided xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] 5950.27 1.08663 6465.72
Subtracted phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] 5489.99 496.64 5986.63
1201 Divided thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] 6042.31 1.08651 6565.03
Subtracted 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] 6523.17 496.27 7019.44
1202 Divided porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] 4913.07 1.08648 5337.95
Subtracted kappa b-ras 1. [refseq;acc:nm_020345] 5721.19 496.01 6217.2
1203 Divided 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 1.08638 4696.04
Subtracted i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] 5721.19 496.01 6217.2
1204 Divided 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 1.08635 6459.79
Subtracted snare associated protein snapin. [refseq;acc:nm_012437] 5721.19 496.01 6217.2
1205 Divided glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] 5946.33 1.08635 6459.79
Subtracted phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] 5462.88 495.24 5958.12
1206 Divided asc-1 complex subunit p100. [refseq;acc:nm_032204] 5946.33 1.08635 6459.79
Subtracted synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] 5460.49 494.13 5954.62
1207 Divided 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] 5946.33 1.08635 6459.79
Subtracted orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] 6105.93 493.48 6599.41
1208 Divided meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] 5913.73 1.08628 6423.98
Subtracted orphan nuclear receptor tr2. [swissprot;acc:p13056] 6105.69 493.37 6599.06
1209 Divided 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 1.08609 5887.53
Subtracted dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] 5147.9 493.35 5641.25
1210 Divided 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 1.08603 6962.22
Subtracted mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] 6051.23 492.94 6544.17
1211 Divided gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] 6410.73 1.08603 6962.22
Subtracted similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] 5807.83 492.64 6300.47
1212 Divided hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 4077.89 1.08592 4428.28
Subtracted ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665] 5807.83 492.64 6300.47

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/