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.

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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 1777 to 1826 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
1777	ARHGEF4	rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320]	216.878	214.286	1.0121
1778	ARHGEF9	cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185]
1779	PBX1	pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424]	206.332	203.874	1.01206
1780	no value	germ cell-less. [refseq;acc:nm_022471]	206.335	203.877
1781	PBX3	pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426]	206.332	203.874
1782	C1orf179	hyporthetical protein mgc27169. [refseq;acc:nm_176782]
1783	MEIS1	homeobox protein meis1. [swissprot;acc:o00470]
1784	MEIS2	homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770]
1785	BAG2	bag-family molecular chaperone regulator-2. [swissprot;acc:o95816]
1786	no value	pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425]
1787	PBX4	pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245]
1788	MEIS3	homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687]
1789	RNASEH2A	ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792]	210.997	213.539	1.01205
1790	no value	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388]	203.759	201.349	1.01197
1791		elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	217.866	215.295	1.01194
1792	ELAVL4	elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378]	217.766	215.199	1.01193
1793	NME2P1	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	193.1	190.823
1794	no value	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392]	193.138	190.861
1795	ELAVL2	elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926]	217.724	215.158
1796	TOP2B	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	203.759	201.357
1797	NME2	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531]	193.111	190.834
1798	ELAVL1	elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717]	217.807	215.242	1.01192
1799	ACTN2	alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609]	217.016	214.481	1.01182
1800	DYRK1A	dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627]	217.011		1.0118
1801	CUGBP1	cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879]	217.984	215.441
1802	ELP4	elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040]	217.011	214.481
1803	DYRK1B	dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463]
1804	CUGBP2	cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561]	217.984	215.442
1805	ACTN4	alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707]	217.008	214.482	1.01178
1806	ACTN1	alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814]	217.009
1807	RALGPS1	ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636]	211.102	208.651	1.01175
1808	RALGPS2	ral-a exchange factor ralgps2. [refseq;acc:nm_152663]
1809	STUB1	stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861]
1810	no value	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]	223.214	225.827	1.01171
1811	GALNT2	polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481]	216.854	214.35	1.01168
1812	CCNC	cyclin c. [swissprot;acc:p24863]	217.071	214.564
1813	GALNTL1	similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428]	216.854	214.35
1814	PPP1CC	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	122.3	123.727	1.01167
1815	no value	dpy-30-like protein. [swissprot;acc:q9c005]	220.462	217.926	1.01164
1816	RAB11FIP1	rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151]
1817	RAB11FIP5	gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470]
1818	COX4NB	neighbor of cox4. [swissprot;acc:o43402]
1819	C14orf122	protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6]
1820	ATP9A	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]
1821	RBM38	rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9]	218.36	215.874	1.01152
1822	PFKL	6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858]	240.32	243.085	1.01151
1823	FXR2	fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116]	202.386	200.086	1.0115
1824	CAPZA1	f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907]	214.722	212.281
1825	FXR1	fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114]	202.386	200.086
1826	NUP43	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	202.393	200.094	1.01149

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
- Hugo is the HGNC identifier if it exists
- 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.