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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4358 to 4407 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
545 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Ranked Subtracted 58 44 14
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] Measured Divided 3889.27 4426.74 1.13819
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Squared Subtracted 25945.4 30892.3 4946.9
546 atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] Divided 27162.5 32347.5 1.19089
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Measured Subtracted 6228.39 7013.19 784.8
electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] Squared 26334.7 31272.3 4937.6
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Rooted Divided 66.082 71.6526 1.0843
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Ranked Subtracted 112 126 14
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Rooted 64.75 69.8065 5.0565
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Ranked Divided 207.222 194.262 1.06671
zinc finger protein t86. [swissprot;acc:o00488] Measured 4052.77 4612.54 1.13812
547 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Ranked Subtracted 234.106 248.104 13.998
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Rooted 64.4927 69.539 5.0463
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Measured 6228.39 7013.19 784.8
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Rooted Divided 66.082 71.6525 1.0843
hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Squared Subtracted 26570.7 31504.6 4933.9
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Ranked Divided 207.26 194.346 1.06645
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Squared 25945.4 30892.3 1.19067
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Measured 5291.92 6020.19 1.13762
548 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 8268.19 9405.85 1.13759
dendritic cell protein. [refseq;acc:nm_006360] Rooted Subtracted 63.847 68.8873 5.0403
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Measured 6228.39 7013.19 784.8
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Rooted Divided 66.082 71.6525 1.0843
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Ranked Subtracted 222.156 208.201 13.955
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Divided 207.26 194.346 1.06645
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Squared Subtracted 26570.7 31504.6 4933.9
vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] Divided 27516.2 32720 1.18912
549 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] Subtracted 26570.7 31504.6 4933.9
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] Measured Divided 5865.79 6671.23 1.13731
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Ranked Subtracted 222.156 208.201 13.955
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Measured 6228.42 7013.21 784.79
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Rooted Divided 66.082 71.6526 1.0843
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Subtracted 63.847 68.8873 5.0403
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Ranked Divided 207.26 194.346 1.06645
vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] Squared 27516.2 32720 1.18912
550 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] Rooted Subtracted 63.847 68.8873 5.0403
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Measured 6228.97 7013.53 784.56
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Rooted Divided 66.082 71.6525 1.0843
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Ranked Subtracted 222.156 208.201 13.955
prohibitin. [swissprot;acc:p35232] Measured Divided 5773.45 6563.69 1.13687
translation initiation factor if-2. [swissprot;acc:o60841] Squared Subtracted 24031.6 28929.7 4898.1
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Ranked Divided 207.26 194.346 1.06645
vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] Squared 27516.2 32720 1.18912
551 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Measured Subtracted 6503.1 7282.94 779.84
cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] Squared Divided 27516.2 32720 1.18912
cpz gene product. [refseq;acc:nm_003652] Rooted Subtracted 63.847 68.8873 5.0403
cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] Squared 26583.8 31468.6 4884.8
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Rooted Divided 66.082 71.6525 1.0843
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Ranked 207.261 194.347 1.06645
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Measured 5773.45 6563.69 1.13687

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/