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 2180 to 2229 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
545 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
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Rooted 66.082 71.6523 1.08429
553 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Ranked 207.26 194.346 1.06645
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Rooted 66.082 71.6523 1.08429
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Measured 3853.64 4379.71 1.13651
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Squared 27516.2 32720 1.18912
554 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Rooted 66.0829 71.6462 1.08419
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Measured 14830.5 13050.3 1.13641
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Squared 8426.68 10010.8 1.18799
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Ranked 207.26 194.346 1.06645
555 proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Squared 8426.68 10010.8 1.18799
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Measured 6167.93 7007.7 1.13615
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Rooted 59.7823 64.7895 1.08376
556 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Ranked 207.27 194.368 1.06638
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Squared 8426.68 10010.8 1.18799
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Measured 6167.93 7007.7 1.13615
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Rooted 66.0911 71.6061 1.08345
557 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Squared 8426.68 10010.8 1.18799
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Ranked 207.272 194.371 1.06637
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Measured 6167.93 7007.7 1.13615
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Rooted 97.1967 105.302 1.08339
558 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 66.1583 71.6729 1.08335

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/