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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 3180 to 3229 of 29840 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	Value Type	description	red	Filtered	network_comparison	green
398	Ranked	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	218.818	1	1.0893	238.358
	Squared	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	18929.1		1.22683	23222.8
		transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	414704	0	1.07396	386144
	Rooted	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	116.707	1	1.10055	106.044
		transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	15.7266	0	1.03394	15.2103
399	Measured	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	548.5		1.03981	527.5
		neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	5201.41	1	1.16109	4479.76
	Ranked	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	207.889		1.08821	226.226
		glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]	16703.1	0	1.03402	17271.4
	Squared	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	18929.1	1	1.22683	23222.8
		protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]	103.239	0	1.072	110.672
	Rooted	cyclin g2. [swissprot;acc:q16589]	116.707	1	1.10055	106.044
		intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	30.8601	0	1.03317	29.8694
400	Measured	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	5201.41	1	1.16109	4479.76
		myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	548.5	0	1.03981	527.5
	Ranked	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410]	16711		1.03395	17278.4
		phosducin-like protein (phlp). [swissprot;acc:q13371]	207.908	1	1.08807	226.218
	Squared	glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807]	39478.8		1.22646	48419
		voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	19277.3	0	1.07133	20652.4
	Rooted	cyclin g1 (cyclin g). [swissprot;acc:p51959]	116.707	1	1.10055	106.044
		mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683]	19.8872	0	1.03295	19.2528
401	Measured	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	5201.41	1	1.16109	4479.76
		myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	548.5	0	1.03981	527.5
	Ranked	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]	207.908	1	1.08807	226.218
		transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	12305.9	0	1.03368	11904.9
	Squared	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	33044.3	1	1.22638	40524.8
		camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]	3862.64	0	1.07096	4136.72
	Rooted	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655]	21.8861		1.0328	22.6039
		serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]	116.707	1	1.10055	106.044
402	Measured	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	5201.41		1.16109	4479.76
		myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	548.5	0	1.03981	527.5
	Ranked	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	10562.4		1.03367	10918
		replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]	207.908	1	1.08807	226.218
	Squared	brain protein 16. [refseq;acc:nm_016458]	2538.95	0	1.07049	2371.77
		endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]	39472	1	1.22601	48393.1
	Rooted	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	21.6987	0	1.03273	22.4088
		eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537]	50.1918	1	1.10037	55.2294
403	Measured	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	5201.41		1.16109	4479.76
		myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	548.5	0	1.03981	527.5
	Ranked	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]	207.908	1	1.08807	226.218
		udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	9783.63	0	1.03348	10111.2
	Squared	glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]	39463.9	1	1.22548	48362.1
		ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	1872.12	0	1.06679	1754.91
	Rooted	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	59.6834	1	1.10037	65.6741
		poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	19.4322	0	1.03267	20.0671
404	Measured	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	5201.41	1	1.16109	4479.76
		thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	1229.57	0	1.03968	1278.36
	Ranked	dna repair protein rad52 homolog. [swissprot;acc:p43351]	207.908	1	1.08807	226.218
		udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	9783.63	0	1.03348	10111.2
	Squared	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	26819.1	1	1.22507	32855.4

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.