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 6358 to 6407 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
398	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Squared	Divided	1	18929.1	23222.8	1.22683
	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]		Subtracted		26157.6	20236.2	5921.4
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Ranked	Divided		218.818	238.358	1.0893
	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]		Subtracted	0	9953.39	10320.9	367.51
	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]			1	207.908	226.218	18.31
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	Squared		0	10.974	2.38124	8.59276
	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]	Rooted	Divided	1	116.707	106.044	1.10055
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]			0	15.7266	15.2103	1.03394
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Squared			414704	386144	1.07396
	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	Measured	Subtracted		112.666	141.702	29.036
	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]		Divided	1	5084.26	5904.1	1.16125
399	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Ranked	Subtracted	0	7670	7311	359
	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]		Divided	1	207.889	226.226	1.08821
	cyclin g2. [swissprot;acc:q16589]	Rooted			116.707	106.044	1.10055
	dna repair protein rad52 homolog. [swissprot;acc:p43351]	Ranked	Subtracted		207.908	226.218	18.31
	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]		Divided	0	16703.1	17271.4	1.03402
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	Rooted			30.8601	29.8694	1.03317
	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	Squared		1	18929.1	23222.8	1.22683
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Measured		0	548.5	527.5	1.03981
	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]			1	5201.41	4479.76	1.16109
	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]	Squared		0	103.239	110.672	1.072
			Subtracted				7.433
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Rooted			2.64575	3.38392	0.73817
	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]	Measured			107	78	29
	thymic stromal co-transporter. [refseq;acc:nm_033051]	Squared		1	26157.6	20236.2	5921.4
	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Rooted			63.2134	69.352	6.1386
	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Measured			4633.92	5572.85	938.93
400	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]		Divided		5201.41	4479.76	1.16109
	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	Ranked	Subtracted		207.931	226.209	18.278
	cyclin g1 (cyclin g). [swissprot;acc:p51959]	Rooted	Divided		116.707	106.044	1.10055
	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	Ranked	Subtracted	0	12581.7	12224.2	357.5
	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410]		Divided		16711	17278.4	1.03395
	glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807]	Squared		1	39478.8	48419	1.22646
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Measured	Subtracted		1834.73	895.893	938.837
		Rooted		0	15.4361	14.7003	0.7358
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]			1	79.931	86.0693	6.1383
	lats homolog 1. [refseq;acc:nm_004690]	Squared		0	12.5892	5.42219	7.16701
	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]	Rooted	Divided		19.8872	19.2528	1.03295
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Measured			548.5	527.5	1.03981
	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9]	Squared	Subtracted	1	33024.9	38867.8	5842.9
	phosducin-like protein (phlp). [swissprot;acc:q13371]	Ranked	Divided		207.908	226.218	1.08807
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Measured	Subtracted	0	65.2968	37.693	27.6038
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Squared	Divided		19277.3	20652.4	1.07133
401	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	Measured		1	5201.41	4479.76	1.16109
	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	Rooted	Subtracted	0	17.8274	17.1002	0.7272
	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	Squared	Divided	1	33044.3	40524.8	1.22638
	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]			0	3862.64	4136.72	1.07096
	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]	Rooted			21.8861	22.6039	1.0328
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Measured	Subtracted	1	1835.3	896.972	938.328
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]			0	1549.26	1522.06	27.2

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.