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

Results: HTML CSV LaTeX

Showing element 130 to 179 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
9	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Measured	Subtracted	0	12478	14756	2278
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Divided		85	6410	75.4118
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Ranked	Subtracted		22286	13216	9070
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]			1	288	362	74
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted			145.551	168.796	23.245
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]			0	126.359	111.067	15.292
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Measured		1	21185	28492	7307
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Squared			256169	162517	93652
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		Divided	0	0.852071	0.00001	85207.1
		Rooted			7.74597		774597
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured		1	398.5	1281.5	3.21581
		Squared			37.5863	388.696	10.3414
		Rooted			19.9625	35.798	1.79326
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Ranked		0	11525	21888	1.89918
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]			1	212	309	1.45755
10	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Squared	Subtracted	0	176989	155919	21070
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Ranked	Divided		7509.39	14178.1	1.88805
		Rooted	Subtracted		54.2583	40.2058	14.0525
	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	Squared	Divided		0.00001	0.823905	82390.5
		Rooted				7.68115	768115
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Measured			85	6410	75.4118
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Squared	Subtracted	1	219048	129762	89286
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Measured		0	7830.62	6193.07	1637.55
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]			1	21185	28492	7307
	protein x 0004. [refseq;acc:nm_016301]	Ranked	Divided		212	309	1.45755
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		Subtracted	0	20989	12479	8510
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]			1	288	362	74
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Measured	Divided		398.5	1281.5	3.21581
		Squared			37.5863	388.696	10.3414
		Rooted			19.9625	35.798	1.79326
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		Subtracted		51.6817	29.5127	22.169
11	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Ranked		0	12170.7	20670.6	8499.9
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Measured			5734.28	7252.02	1517.74
	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]		Divided	1	398.5	1281.5	3.21581
		Squared			37.5863	388.696	10.3414
		Rooted			19.9625	35.798	1.79326
	db83 protein. [swissprot;acc:p57088]	Ranked	Subtracted		288	362	74
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Rooted		0	12.3693	25.7294	13.3601
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Squared		1	219048	129762	89286
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Measured			21185	28492	7307
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Squared		0	54383.4	34012.2	20371.2
	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	Ranked	Divided		11627	6248	1.86092
	protein x 0004. [refseq;acc:nm_016301]	Rooted	Subtracted	1	51.6817	29.5127	22.169
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	Divided		337	232	1.45259
	sedlin. [swissprot;acc:o14582]	Squared		0	0.00001	0.437633	43763.3
		Rooted				6.55744	655744
	serpin b12. [swissprot;acc:q96p63]	Measured			199.549	5.56738	35.8425
12	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	Rooted	Subtracted		21.3967	34.6716	13.2749
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Squared			1.73869	19295.9	19294.2
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Rooted		1	80.4705	101.526	21.0555

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.