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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 3180 to 3229 of 14920 in total

Interaction Map

: High confidence
Network Comparison Type

: Divided

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

- http://analysis.yellowcouch.org/