MK5 Microarray Data

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

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Showing element 2901 to 2950 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
1451	my016 protein. [sptrembl;acc:q9h3k6]	Divided	224.755	229.2	1.01978
	sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422]	Subtracted	207.024	211.089	4.065
1452	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Divided	160.381	163.554	1.01978
	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	Subtracted	212.001	207.937	4.064
1453	eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223]		207.024	211.086	4.062
	reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3]	Divided	207.038	211.13	1.01976
1454	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	Subtracted	240.077	236.015	4.062
	sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422]	Divided	207.024	211.089	1.01964
1455	eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9]			211.085	1.01962
	eh-domain containing protein 2. [swissprot;acc:q9nzn4]	Subtracted		211.086	4.062
1456	eh-domain containing protein 3. [swissprot;acc:q9nzn3]
	eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223]	Divided			1.01962
1457	eh-domain containing protein 2. [swissprot;acc:q9nzn4]
	transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595]	Subtracted	215.328	211.267	4.061
1458	eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9]		207.024	211.085
	eh-domain containing protein 3. [swissprot;acc:q9nzn3]	Divided		211.086	1.01962
1459	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060]		192.336	188.637	1.01961
	reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799]	Subtracted	207.019	211.077	4.058
1460	arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815]		215.122	211.066	4.056
	thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669]	Divided	205.817	209.851	1.0196
1461	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	Subtracted	171.231	167.177	4.054
	reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799]	Divided	207.019	211.077	1.0196
1462	dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957]		205.817	209.851
	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	Subtracted	171.231	167.177	4.054
1463	pnas-18. [sptrembl;acc:q9bzu3]	Divided	161.056	164.211	1.01959
	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]	Subtracted	171.231	167.177	4.054
1464	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Divided	217.351	213.18	1.01957
	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	Subtracted	171.231	167.177	4.054
1465	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]
	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	Divided	217.351	213.18	1.01957
1466	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	Subtracted	171.231	167.177	4.054
	reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298]	Divided	207.022	211.073	1.01957
1467	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]		228.513	232.983	1.01956
	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	Subtracted	171.231	167.177	4.054
1468	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	Divided	212.001	207.937	1.01954
	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	Subtracted	171.231	167.177	4.054
1469	reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197]	Divided	207.013	211.05	1.0195
	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]	Subtracted	171.231	167.177	4.054
1470	glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897]	Divided	221.412	217.199	1.0194
	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]	Subtracted	171.231	167.177	4.054
1471	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]
	spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623]	Divided	221.412	217.199	1.0194
1472	glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]	Subtracted	171.231	167.177	4.054
1473	glutamyl trna synthetase. [sptrembl;acc:o14563]	Divided	221.412	217.199	1.0194
	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]	Subtracted	171.231	167.177	4.054
1474	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410]	Divided	218.582	214.427	1.01938
	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]	Subtracted	171.231	167.177	4.054
1475	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Divided	181.882	178.438	1.0193
	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]	Subtracted	171.231	167.177	4.054

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.