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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
795 ubiquitin-conjugating enzyme e2-32 kda complementing (ec 6.3.2.19) (ubiquitin-protein ligase) (ubiquitin carrier protein) (e2-cdc34). [swissprot;acc:p49427] Subtracted Low confidence 199.792 194.573 5.219
796 beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] High confidence 212.386 221.785 9.399
grancalcin. [swissprot;acc:p28676] Divided Low confidence 202.524 197.308 1.02644
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] High confidence 224.244 234.511 1.04578
rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640] Subtracted Low confidence 202.755 197.536 5.219
797 asc-1 complex subunit p100. [refseq;acc:nm_032204] Divided 211.636 206.184 1.02644
calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Subtracted 202.525 197.308 5.217
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Divided High confidence 224.244 234.511 1.04578
syntaxin 16 (syn16). [swissprot;acc:o14662] Subtracted 212.386 221.785 9.399
798 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
grancalcin. [swissprot;acc:p28676] Low confidence 202.524 197.308 5.216
leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Divided High confidence 224.244 234.511 1.04578
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Low confidence 202.524 197.308 1.02644
799 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Subtracted 206.243 201.027 5.216
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Divided 201.294 196.11 1.02643
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] High confidence 221.965 212.404 1.04501
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Subtracted 212.386 221.785 9.399
800 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Low confidence 206.244 201.028 5.216
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Divided High confidence 221.965 212.404 1.04501
rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640] Low confidence 202.755 197.536 1.02642
801 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] Subtracted High confidence 212.386 221.785 9.399
beta-catenin (pro2286). [swissprot;acc:p35222] Divided 224.445 214.894 1.04445
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Low confidence 202.522 197.311 1.02641
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Subtracted 202.524 197.308 5.216
802 dc12 protein. [refseq;acc:nm_020187] Divided 203.345 198.117 1.02639
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Subtracted High confidence 212.386 221.785 9.399
testis-specific protein tex28. [swissprot;acc:o15482] Divided 1.04425
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Subtracted Low confidence 201.338 196.126 5.212
803 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kda subunit precursor (ec 2.4.1.119) (ribophorin i) (rpn-i). [swissprot;acc:p04843] Divided 199.573 194.441 1.02639
olf-1/ebf associated zinc finger protein; smad- and olf-interacting zinc finger protein. [refseq;acc:nm_015069] Subtracted 204.922 199.711 5.211
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Divided High confidence 212.386 221.785 1.04425
syntaxin 1b. [swissprot;acc:q15531] Subtracted 9.399
804 a kindred of iglon. [refseq;acc:nm_173808] Divided 1.04425
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Low confidence 204.519 199.267 1.02636
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Subtracted High confidence 212.386 221.785 9.399
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Low confidence 202.522 197.311 5.211
805 ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Divided High confidence 212.386 221.785 1.04425
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Subtracted 9.399
early hematopoietic zinc finger. [refseq;acc:nm_015461] Low confidence 204.914 199.706 5.208
synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Divided 198.496 193.399 1.02635
806 inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] High confidence 212.386 221.785 1.04425
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Subtracted 267.447 276.773 9.326
mosaic protein lgn. [swissprot;acc:p81274] Low confidence 207.56 202.355 5.205
vacuolar atp synthase subunit c (ec 3.6.3.14) (v-atpase c subunit) (vacuolar proton pump c subunit). [swissprot;acc:p21283] Divided 202.369 197.173 1.02635
807 myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] 200.782 195.631 1.02633
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Subtracted 203.907 198.706 5.201
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Divided High confidence 212.386 221.785 1.04425
trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] Subtracted 218.521 227.796 9.275
808 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 223.186 213.912 9.274

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/