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 Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 1575 to 1624 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
788 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Low confidence 200.788 195.605 1.0265
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] High confidence 138.705 132.538 1.04653
789 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 224.244 234.511 1.04578
polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] Low confidence 205.859 200.547 1.02649
790 40s ribosomal protein s21. [swissprot;acc:p35265] High confidence 224.244 234.511 1.04578
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Low confidence 200.79 195.608 1.02649
791 cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] High confidence 224.244 234.511 1.04578
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] Low confidence 205.859 200.547 1.02649
792 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 204.204 198.939 1.02647
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] High confidence 224.244 234.511 1.04578
793 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]
similar to atp/gtp-binding protein. [sptrembl;acc:q8nem8] Low confidence 184.195 179.447 1.02646
794 plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] High confidence 224.244 234.511 1.04578
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Low confidence 184.195 179.447 1.02646
795 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 202.525 197.308 1.02644
serpin b11. [swissprot;acc:q96p15] High confidence 224.244 234.511 1.04578
796 grancalcin. [swissprot;acc:p28676] 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
797 asc-1 complex subunit p100. [refseq;acc:nm_032204] Low confidence 211.636 206.184 1.02644
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] High confidence 224.244 234.511 1.04578
798 leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Low confidence 202.524 197.308 1.02644
799 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 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
800 nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]
rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640] Low confidence 202.755 197.536 1.02642
801 beta-catenin (pro2286). [swissprot;acc:p35222] High confidence 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
802 dc12 protein. [refseq;acc:nm_020187] 203.345 198.117 1.02639
testis-specific protein tex28. [swissprot;acc:o15482] High confidence 212.386 221.785 1.04425
803 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kda subunit precursor (ec 2.4.1.119) (ribophorin i) (rpn-i). [swissprot;acc:p04843] Low confidence 199.573 194.441 1.02639
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] High confidence 212.386 221.785 1.04425
804 a kindred of iglon. [refseq;acc:nm_173808]
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Low confidence 204.519 199.267 1.02636
805 ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] High confidence 212.386 221.785 1.04425
synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Low confidence 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
vacuolar atp synthase subunit c (ec 3.6.3.14) (v-atpase c subunit) (vacuolar proton pump c subunit). [swissprot;acc:p21283] Low confidence 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
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] High confidence 212.386 221.785 1.04425
808 beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]
vigilin (high density lipoprotein-binding protein) (hdl-binding protein). [swissprot;acc:q00341] Low confidence 201.169 196.014 1.0263
809 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] 202.744 197.552 1.02628
syntaxin 16 (syn16). [swissprot;acc:o14662] High confidence 212.386 221.785 1.04425
810 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] Low confidence 196.326 191.3 1.02627
811 syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] High confidence 212.386 221.785 1.04425
syntaxin 1b. [swissprot;acc:q15531] Low confidence 211.432 206.021 1.02626
812 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920] High confidence 212.386 221.785 1.04425
zinc transporter 1 (znt-1). [swissprot;acc:q9y6m5] Low confidence 206.173 200.909 1.0262

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/