Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 3180 to 3229 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

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

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.

- http://analysis.yellowcouch.org/