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

Results: HTML CSV LaTeX

Showing element 325 to 374 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
163	ARRB2	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Subtracted	133	105	28	
163	SNF8	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Divided	209.299	249.187	1.19058	
164	ARRB1	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Subtracted	133	105	28	
164	SLC39A6	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Divided	209.299	249.187	1.19058	
165	GAD2	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Divided	209.299	249.187	1.19058	
165	SPATA6	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Subtracted	133	105	28	
166	NAPG	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Divided	209.299	249.187	1.19058	
166	NEUROD4	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Subtracted	312	284	28	
167	AMPD2	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Subtracted	133	105	28	
167	GAD1	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	Divided	209.299	249.187	1.19058	
168		gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Divided	82.5916	98.0548	1.18722	
168	CHD5	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Subtracted	312	284	28	
169	ATG3	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Divided	82.5916	98.0548	1.18722	
169	CDK2AP1	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	Subtracted	312	284	28	
170	PRPF40B	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Subtracted	227.971	200.417	27.554	
170	TIA1	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Divided	227.199	192.715	1.17894	
171	TIAL1	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Divided	227.202	192.823	1.17829	
171	TRPC4	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	Subtracted	201.478	228.784	27.306	
172	TBC1D10A	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	Subtracted	201.515	228.752	27.237	
172	TIPRL	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [source:refseq;acc:nm_152902]	Divided	174.667	205.556	1.17685	
173	SNRPD1	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Divided	227.032	193.056	1.17599	
173	TRPC5	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	Subtracted	201.515	228.752	27.237	
174	DGCR14	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Divided	335	286	1.17133	
174	LUC7L2	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Subtracted	228.1	200.968	27.132	
175	COPS3	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Divided	199.949	234.187	1.17123	
175	LUC7L	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Subtracted	228.085	201.006	27.079	
176	EIF5	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Subtracted	271.016	244.167	26.849	
176	POLE4	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Divided	275.754	235.908	1.1689	
177	NCBP2L	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Divided	229.406	196.695	1.1663	
177	SIN3A	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Subtracted	241.07	267.88	26.81	
178		formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Divided	226.887	194.72	1.1652	
178	DENR	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Subtracted	241.07	267.88	26.81	
179		huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Divided	226.884	194.79	1.16476	
179	PAH	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	Subtracted	227.357	254.15	26.793	
180	DUS1L	pp3111 protein. [source:refseq;acc:nm_022156]	Subtracted	227.357	254.15	26.793	
180	TARDBP	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Divided	256.228	298.438	1.16474	
181	B9D1	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Divided	229.818	267.265	1.16294	
181	STX18	syntaxin 18. [source:swissprot;acc:q9p2w9]	Subtracted	227.357	254.15	26.793	
182		rd protein. [source:swissprot;acc:p18615]	Subtracted	227.357	254.15	26.793	
182	HAT1	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Divided	277.546	240.461	1.15422	
183	GSTO1	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	Subtracted	227.357	254.15	26.793	
183	NCBP2	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Divided	228.306	198.011	1.153	
184	AIG1	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	Subtracted	227.357	254.15	26.793	
184	OSR1	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	Divided	274.027	237.79	1.15239	
185	ADIPOR2	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Divided	281.582	246.371	1.14292	
185	ATP5F1	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	Subtracted	227.357	254.15	26.793	
186	DNAJC12	j domain containing protein 1. [source:swissprot;acc:q9ukb3]	Subtracted	227.357	254.15	26.793	
186	FLNB	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [source:refseq;acc:nm_001457]	Divided	226.582	198.444	1.14179	
187	REV1	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Divided	226.582	198.444	1.14179	
187	SNX13	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [source:swissprot;acc:q9y5w8]	Subtracted	227.357	254.15	26.793	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/