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

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Showing element 6612 to 6661 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
414	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Squared	Subtracted	0	14.0914	8.90793	5.18347
	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]	Squared	Subtracted	1	32192.8	37967.1	5774.3
	germ cell-less. [refseq;acc:nm_022471]	Ranked	Divided	0	10978.8	10644.4	1.03142
	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]	Ranked	Subtracted	0	9783.63	10111.2	327.57
	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Rooted	Divided	1	55.5489	50.535	1.09922
	katanin p60 subunit a 1. [refseq;acc:nm_007044]	Ranked	Divided		232.431	252.238	1.08522
	max protein. [swissprot;acc:p25912]	Ranked	Subtracted		227.828	210.561	17.267
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Rooted	Divided	0	6.9282	7.14143	1.03078
	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	Squared	Divided		151156	159204	1.05324
	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	Subtracted		19.8872	19.2528	0.6344
	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Measured	Subtracted	1	5051.16	5975.51	924.35
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]		Divided	0	7520.78	7276.12	1.03363
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]		Subtracted	0	125.5	103.5	22
415	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	Rooted	Divided	1	55.5489	50.535	1.09922
	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	Squared	Subtracted	0	246.531	241.387	5.144
	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]	Squared		1	32192.6	37966.9	5774.3
	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866]	Rooted			62.574	68.4128	5.8388
	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	Measured			7725.1	8647.74	922.64
	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Ranked	Divided		232.382	252.166	1.08514
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	Measured	Subtracted	0	86	64	22
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Rooted	Divided		6.9282	7.14143	1.03078
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Rooted	Subtracted		22.1458	22.7768	0.631
	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	Squared	Divided		82695.1	87060.9	1.05279
	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	Ranked	Divided		13571.2	13166.3	1.03075
	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]		Subtracted	1	200.586	183.423	17.163
	udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537]		Subtracted	0	9783.63	10111.2	327.57
	vav-3 protein. [swissprot;acc:q9ukw4]	Measured	Divided	1	6647.43	7706.18	1.15927
	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	Squared		1	29160.4	35570.2	1.21981
	zinc finger protein 232. [swissprot;acc:q9uny5]	Measured		0	721.814	699.215	1.03232
416	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	Rooted		1	55.5489	50.535	1.09922
	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	Ranked		1	240.6	261.041	1.08496
	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	Squared	Subtracted	0	5.83408	0.742249	5.09183
	human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]	Measured		1	7725.1	8647.74	922.64
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Squared		1	32192.5	37966.8	5774.3
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Rooted	Divided	0	6.9282	7.14143	1.03078
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Measured	Subtracted		548.5	527.5	21
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Rooted	Subtracted		22.1458	22.7768	0.631
	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	Measured	Divided	1	4509.54	5223.95	1.15842
	prohibitin. [swissprot;acc:p35232]	Squared	Divided		22841.8	27856.2	1.21953
	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903]	Rooted	Subtracted		62.574	68.4128	5.8388
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Squared	Divided	0	110701	116507	1.05245
	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	Ranked	Subtracted	1	200.791	183.66	17.131
	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]		Divided	0	13607.6	13202	1.03072
	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]		Subtracted		9783.63	10111.2	327.57
	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	Measured	Divided		721.888	699.297	1.03231
417	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]	Measured	Divided	1	4522.71	5233.14	1.15708
	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]	Squared	Subtracted	1	32192.8	37967.1	5774.3
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Ranked		0	14570.4	14247.3	323.1
	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566]	Rooted		1	62.574	68.4128	5.8388
	j domain containing protein 1. [swissprot;acc:q9ukb3]	Rooted	Divided	1	55.5489	50.535	1.09922

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/