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 2158 to 2207 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
540 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Rooted 66.082 71.6526 1.0843
gk001 protein. [refseq;acc:nm_020198] Measured 10603.5 12069.4 1.13825
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Ranked 222.156 208.201 1.06703
541 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Measured 10600.3 12065.2 1.13819
coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Squared 53774.6 45105.5 1.1922
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Ranked 222.156 208.201 1.06703
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Rooted 66.082 71.6526 1.0843
542 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Ranked 222.156 208.201 1.06703
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Measured 3889.27 4426.74 1.13819
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Squared 26084.2 31084.3 1.19169
543 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Measured 10599.9 12064.7 1.13819
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Rooted 66.082 71.6525 1.0843
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Squared 26612.5 31709 1.19151
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Ranked 222.156 208.201 1.06703
544 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Rooted 66.082 71.6525 1.0843
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] Ranked 222.156 208.201 1.06703
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] Measured 3889.27 4426.74 1.13819
ran binding protein 11. [refseq;acc:nm_016338] Squared 26018.9 30994.1 1.19121
545 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Ranked 248.866 233.287 1.06678
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Rooted 66.082 71.6526 1.0843
membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Squared 26010 30981.7 1.19115
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 3889.27 4426.74 1.13819
546 atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] Squared 27162.5 32347.5 1.19089
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Rooted 66.082 71.6526 1.0843
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Ranked 207.222 194.262 1.06671
zinc finger protein t86. [swissprot;acc:o00488] Measured 4052.77 4612.54 1.13812
547 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Rooted 66.082 71.6525 1.0843
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Ranked 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
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Rooted 66.082 71.6525 1.0843
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Ranked 207.26 194.346 1.06645
vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] Squared 27516.2 32720 1.18912
549 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 5865.79 6671.23 1.13731
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Rooted 66.082 71.6526 1.0843
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Ranked 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 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Rooted 66.082 71.6525 1.0843
prohibitin. [swissprot;acc:p35232] Measured 5773.45 6563.69 1.13687
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Ranked 207.26 194.346 1.06645
vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] Squared 27516.2 32720 1.18912
551 cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Rooted 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
552 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Squared 27516.2 32720 1.18912
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Measured 15427.2 13572.8 1.13663
crk-like protein. [swissprot;acc:p46109] Ranked 207.26 194.346 1.06645

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/