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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Gene	Network Comparison Type	red	Value Type	green	Rank	Interaction Map	description	Filtered	network_comparison

Results: HTML CSV LaTeX

Showing element 1358 to 1407 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

red	green	Rank	description	network_comparison
5369.43	5738.73	1706	translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50]	1.06878
5372.25	5775.21	1482	leng5 protein. [refseq;acc:nm_024075]	1.07501
		1483	tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381]
		1484	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]
		1485	tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6]
		1486	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]
5379.03	5659.64	2162	tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897]	1.05217
5379.33	5660	2161	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610]	1.05218
5379.49	5660.18	2159	serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896]
5379.55	5660.25	2160	activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259]
5384.41	6012.82	724	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	1.11671
		725	phenylalanine-trna synthetase. [refseq;acc:nm_006567]
5384.89	5746.51	1750	arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144]	1.06715
5385.04	5933.65	891	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	1.10188
5386.37	5744.89	1774	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	1.06656
		1775	zinc finger protein 258. [refseq;acc:nm_145310]
		1776	zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]
		1777	zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]
		1778	actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]
		1779	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]
		1780	similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]
		1781	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
		1782	zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]
		1783	actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
		1784	arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]
		1785	nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]
		1786	actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]
5386.48	5744.78	1787	interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894]	1.06652
5386.49	5744.76	1788	arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511]	1.06651
5387.64	5743.5	1796	tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7]	1.06605
5390.78	6142.07	521	u4/u6-associated rna splicing factor. [refseq;acc:nm_004698]	1.13937
5391.27	5706.64	2011	hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819]	1.0585
		2012	hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839]
		2013	hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219]
5391.64	5903.72	1004	o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807]	1.09498
5393.37	5909.47	992	putative sialoglycoprotease type 2. [refseq;acc:nm_022353]	1.09569
5394.24	5730.73	1918	seven in absentia homolog 1. [refseq;acc:nm_003031]	1.06238
5396.36	5929.41	919	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	1.09878
5396.61	5733.93	1906	mitochondrial ribosomal protein l18. [refseq;acc:nm_014161]	1.06251
5397.21	5790.45	1547	cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320]	1.07286
5399.47	5737.79	1900	seven in absentia homolog 2. [refseq;acc:nm_005067]	1.06266
5401.39	5838.63	1314	vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7]	1.08095
5406.5	5939.42	924	opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982]	1.09857
5412.23	5913.4	1057	tata element modulatory factor (tmf). [swissprot;acc:p82094]	1.0926
		1058	scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680]
		1061	nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]
		1062	ammecr1 protein. [refseq;acc:nm_015365]
		1063	mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406]
5413.63	5946.46	935	neurotrimin precursor (hnt). [swissprot;acc:q9p121]	1.09842
5414.98	5818.7	1498	40s ribosomal protein s13. [swissprot;acc:q02546]	1.07456

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.