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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2151 to 2200 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
538 Squared integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] 28657.6 34208.6 1.1937
Rooted homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 66.0817 71.6543 1.08433
539 Measured thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] 10603.5 12069.4 1.13825
Ranked protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] 236.964 252.86 1.06708
Squared werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] 20613.1 24595.9 1.19322
Rooted homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 66.0818 71.6537 1.08432
540 Measured gk001 protein. [refseq;acc:nm_020198] 10603.5 12069.4 1.13825
Ranked selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 222.156 208.201 1.06703
Squared argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 26048.6 31057.4 1.19229
Rooted gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 66.082 71.6526 1.0843
541 Measured calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 10600.3 12065.2 1.13819
Ranked flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 222.156 208.201 1.06703
Squared coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] 53774.6 45105.5 1.1922
Rooted forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 66.082 71.6526 1.0843
542 Measured rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 3889.27 4426.74 1.13819
Ranked inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] 222.156 208.201 1.06703
Squared s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] 26084.2 31084.3 1.19169
Rooted gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 66.082 71.6526 1.0843
543 Measured calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 10599.9 12064.7 1.13819
Ranked selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] 222.156 208.201 1.06703
Squared glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] 26612.5 31709 1.19151
Rooted gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 66.082 71.6525 1.0843
544 Measured rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] 3889.27 4426.74 1.13819
Ranked inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] 222.156 208.201 1.06703
Squared ran binding protein 11. [refseq;acc:nm_016338] 26018.9 30994.1 1.19121
Rooted gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 66.082 71.6525 1.0843
545 Measured rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] 3889.27 4426.74 1.13819
Ranked eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 248.866 233.287 1.06678
Squared membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] 26010 30981.7 1.19115
Rooted gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 66.082 71.6526 1.0843
546 Measured zinc finger protein t86. [swissprot;acc:o00488] 4052.77 4612.54 1.13812
Ranked wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 207.222 194.262 1.06671
Squared atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 27162.5 32347.5 1.19089
Rooted interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 66.082 71.6526 1.0843
547 Measured werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] 5291.92 6020.19 1.13762
Ranked proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 207.26 194.346 1.06645
Squared s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] 25945.4 30892.3 1.19067
Rooted gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 66.082 71.6525 1.0843
548 Measured adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 8268.19 9405.85 1.13759
Ranked tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 207.26 194.346 1.06645
Squared vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] 27516.2 32720 1.18912
Rooted gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 66.082 71.6525 1.0843
549 Measured dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] 5865.79 6671.23 1.13731
Ranked proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 207.26 194.346 1.06645
Squared vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] 27516.2 32720 1.18912
Rooted phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 66.082 71.6526 1.0843
550 Measured prohibitin. [swissprot;acc:p35232] 5773.45 6563.69 1.13687
Ranked tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 207.26 194.346 1.06645
Squared vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] 27516.2 32720 1.18912
Rooted gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 66.082 71.6525 1.0843

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/