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 4986 to 5035 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1247 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Rooted 57.8009 55.3045 1.04514
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Measured 6278.76 6807.51 1.08421
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Ranked 219.354 224.7 1.02437
1248 keratin associated protein 4.4. [refseq;acc:nm_032524] 224.699
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Squared 20118.6 22816.7 1.13411
protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] Measured 6275.86 6803.95 1.08415
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Rooted 60.3706 57.7639 1.04513
1249 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Ranked 219.354 224.7 1.02437
atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] Squared 20118.6 22816.8 1.13411
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Rooted 60.3706 57.7637 1.04513
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Measured 4413.55 4784.6 1.08407
1250 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 10733.4 9902.6 1.0839
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] Ranked 219.354 224.7 1.02437
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Squared 20118.6 22816.8 1.13411
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Rooted 60.3706 57.7637 1.04513
1251 cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Squared 20118.6 22816.7 1.13411
integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] Ranked 219.354 224.7 1.02437
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Measured 8618.32 9340.98 1.08385
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Rooted 62.7005 65.5304 1.04513
1252 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] Squared 23843.4 27039 1.13402
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Rooted 60.3706 57.7638 1.04513
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] Ranked 219.354 224.7 1.02437
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Measured 8618.32 9340.98 1.08385
1253 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Squared 14996.8 17006.2 1.13399
ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] Ranked 219.354 224.7 1.02437
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Rooted 60.3736 57.7709 1.04505
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Measured 8618.32 9340.98 1.08385
1254 dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] Squared 26773.9 30358.8 1.1339
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Measured 10725.6 9896.32 1.0838
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Ranked 219.354 224.7 1.02437
serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] Rooted 62.4299 65.2404 1.04502
1255 gtp binding protein 2. [refseq;acc:nm_019096]
mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Squared 22337.6 25320.9 1.13356
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Ranked 219.354 224.7 1.02437
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] Measured 5438.66 5893.87 1.0837
1256 cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] Rooted 62.4299 65.2404 1.04502
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Measured 10719 9891.08 1.0837
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Ranked 219.354 224.699 1.02437
transportin-sr; importin 12. [refseq;acc:nm_012470] Squared 22037.5 24968.1 1.13298
1257 dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] Rooted 62.4299 65.2404 1.04502
espin. [refseq;acc:nm_031475] Ranked 219.354 224.7 1.02437
exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Squared 22008 24929.4 1.13274
immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] Measured 5438.66 5893.87 1.0837
1258 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] Squared 23019.8 26073.1 1.13264
cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] Ranked 219.354 224.7 1.02437
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Measured 6251.32 6774.12 1.08363
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] Rooted 62.4299 65.2404 1.04502
1259 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Squared 13834.4 15664 1.13225
cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] Rooted 62.4299 65.2404 1.04502
epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Measured 5685.38 6157.7 1.08308

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/