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 7062 to 7111 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
442	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	Squared	Subtracted	1	33908.1	39510.9	5602.8
	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	Rooted	Divided	0	29.7464	29.0619	1.02355
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Squared			18476.6	19091.9	1.0333
	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	Measured	Subtracted		42	56	14
	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]	Rooted		1	66.082	71.6523	5.5703
	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	Measured			5189	6088.47	899.47
	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]		Divided	0	6699.82	6856.28	1.02335
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	Squared	Subtracted		2.70982	1.44	1.26982
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Measured	Divided	1	6251.99	7192.17	1.15038
	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	Rooted	Subtracted	0	35.7784	35.3221	0.4563
	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]		Divided	1	63.2134	69.352	1.09711
443	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]				50.1766	45.7369	1.09707
	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	Measured			6252.27	7192.51	1.15038
	calcyphosine. [swissprot;acc:q13938]		Subtracted		5189	6088.47	899.47
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Rooted	Divided	0	19.3683	19.8189	1.02326
			Subtracted				0.4506
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Squared			6791.15	6792.32	1.17
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Ranked			10043.7	9799.17	244.53
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	Squared	Divided		26171.8	27038.8	1.03313
	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]	Ranked		1	223.79	207.539	1.0783
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]			0	9141.6	8940.14	1.02253
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Measured	Subtracted		1	15	14
	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]		Divided		2432.41	2379.52	1.02223
	similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]	Rooted	Subtracted	1	66.082	71.6523	5.5703
	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	Squared			33900.6	39498	5597.4
	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199]		Divided		26472.8	32067.7	1.21135
	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]	Ranked	Subtracted		210.225	226.578	16.353
444	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	Measured	Divided	0	2431.87	2378.99	1.02223
	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	Rooted		1	50.1636	45.7275	1.09701
	alpha crystallin a chain. [swissprot;acc:p02489]	Squared	Subtracted	0	1.27019	2.40686	1.13667
	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]		Divided		3778.75	3670.49	1.02949
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Measured	Subtracted	1	5189	6088.47	899.47
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Ranked	Divided	0	14556.7	14237.8	1.0224
	glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807]	Rooted	Subtracted	1	87.2414	92.8092	5.5678
	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]		Divided	0	42.0329	43.0082	1.0232
	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	Ranked		1	223.801	207.549	1.0783
	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	Measured			3758.67	4322.87	1.15011
	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	Ranked	Subtracted		250.053	233.725	16.328
	serpin b11. [swissprot;acc:q96p15]	Measured		0	42	56	14
	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	Rooted			30.9876	30.5384	0.4492
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Ranked			11290.8	11525.8	235
	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199]	Squared		1	26472.8	32067.7	5594.9
	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965]		Divided		58831	48584.2	1.21091
445	ad24 protein. [refseq;acc:nm_022451]	Measured			3753.71	4315.95	1.14978
	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Rooted	Subtracted	0	4.79583	4.3589	0.43693
	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	Measured			42	56	14
	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	Rooted	Divided		42.0329	43.0082	1.0232
	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	Ranked	Subtracted		10028.5	10261.5	233
	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Measured		1	1857.32	958.237	899.083
	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	Ranked	Divided	0	7965.06	7790.78	1.02237

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.