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 25626 to 25675 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2702 dynein light chain 2. [refseq;acc:nm_080677] Measured Subtracted 5239.33 5260 20.67
importin 8; ran-binding protein 8. [refseq;acc:nm_006390] Ranked 220.521 220.395 0.126
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Squared 314.926 27.2805 287.645
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Ranked Divided 188.435 188.311 1.00066
ral-a exchange factor ralgps2. [refseq;acc:nm_152663] Squared 31182.7 31851.7 1.02145
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Rooted Subtracted 44.585 44.4413 0.1437
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Divided 44.6114 44.4835 1.00288
2703 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] Ranked Subtracted 220.521 220.395 0.126
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Measured Divided 8972.87 9007.71 1.00388
integral membrane protein cii-3b. [sptrembl;acc:o75609] Rooted 65.6868 65.5154 1.00262
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Squared Subtracted 314.926 27.2805 287.645
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Measured 10143.6 10163.6 20
stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] Squared Divided 31182.7 31851.7 1.02145
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Ranked 188.435 188.311 1.00066
zinc finger protein 232. [swissprot;acc:q9uny5] Rooted Subtracted 44.5859 44.4426 0.1433
2704 creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Measured Divided 8980.12 9013.33 1.0037
gk001 protein. [refseq;acc:nm_020198] Ranked 188.435 188.311 1.00066
hsgcn1 (fragment). [sptrembl;acc:q99736] Subtracted 220.521 220.395 0.126
proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618] Squared Divided 34346.5 34937.9 1.01722
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] Subtracted 314.926 27.2805 287.645
succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] Rooted Divided 65.6874 65.5164 1.00261
testis-specific protein tex28. [swissprot;acc:o15482] Measured Subtracted 5603.24 5583.64 19.6
zinc finger protein 305. [swissprot;acc:o43309] Rooted 44.5858 44.4426 0.1432
2705 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] Divided 62.4411 62.5908 1.0024
brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] Ranked Subtracted 220.521 220.395 0.126
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Divided 188.457 188.334 1.00065
db83 protein. [swissprot;acc:p57088] Squared Subtracted 314.926 27.2805 287.645
protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] Measured Divided 4137.61 4152.72 1.00365
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Subtracted 5603.24 5583.64 19.6
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Squared Divided 22233.9 21876.3 1.01635
zinc finger protein 99. [refseq;acc:nm_032164] Rooted Subtracted 44.586 44.4429 0.1431
2706 a kindred of iglon. [refseq;acc:nm_173808] Measured 5603.24 5583.64 19.6
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Ranked Divided 188.459 188.336 1.00065
nucleoporin like 1. [refseq;acc:nm_014089] Squared 30868.3 31361.7 1.01598
peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] Measured 8979.61 9012.31 1.00364
succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] Rooted 65.5744 65.4175 1.0024
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Ranked Subtracted 188.435 188.31 0.125
ubiquitin. [swissprot;acc:p02248] Squared 41247.2 41534.3 287.1
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] Rooted 44.5861 44.443 0.1431
2707 ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Measured 5603.24 5583.64 19.6
calsyntenin-1 precursor. [swissprot;acc:o94985] Ranked 188.435 188.31 0.125
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Squared 2547.12 2286.96 260.16
prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675] Measured Divided 8979.61 9012.31 1.00364
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] Ranked 215.096 215.232 1.00063
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Squared 30868.3 31361.7 1.01598
ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Rooted 74.0281 74.1998 1.00232
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Subtracted 44.5865 44.4436 0.1429
2708 cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] Squared Divided 30868.3 31361.7 1.01598
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Subtracted 2547.12 2286.96 260.16
inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Measured 5603.24 5583.64 19.6

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/