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 4958 to 5007 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1240 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Ranked 219.354 224.7 1.02437
multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Squared 26127.9 29648.4 1.13474
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Measured 5654.54 6132.69 1.08456
1241 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] 6436.19 6980.13 1.08451
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Ranked 219.354 224.7 1.02437
surfeit locus protein 1. [swissprot;acc:q15526] Rooted 62.6939 65.5285 1.04521
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Squared 26204.1 29732 1.13463
1242 hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Ranked 219.354 224.7 1.02437
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Rooted 62.6944 65.5286 1.04521
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Measured 11143.5 10276.3 1.08439
1243 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Rooted 62.6939 65.5285 1.04521
keratin associated protein 1.5. [refseq;acc:nm_031957] Ranked 219.354 224.699 1.02437
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Squared 19239.8 21829.3 1.13459
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Measured 11143.5 10276.3 1.08439
1244 myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Squared 26227.1 29756.6 1.13457
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Rooted 62.6939 65.5285 1.04521
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Measured 4835.55 5243.23 1.08431
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Ranked 219.354 224.7 1.02437
1245 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] Measured 4835.55 5243.23 1.08431
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Rooted 62.6947 65.5287 1.0452
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Ranked 219.354 224.699 1.02437
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Squared 13127 14892.9 1.13452
1246 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Rooted 62.6947 65.5287 1.0452
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Squared 20120.1 22818.6 1.13412
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Ranked 219.354 224.699 1.02437
p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] Measured 5346.11 5796.72 1.08429
1247 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Squared 20117.4 22815.3 1.13411
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

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/