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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 127 to 176 of 3228 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
127	CHMP2A	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	94	114	1.21277	
128	STAMBP	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	94	114	1.21277	
129	VPS24	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	94	114	1.21277	
130	CHMP4A	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	94	114	1.21277	
131	SON	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [source:swissprot;acc:p18583]	294.053	242.562	1.21228	
132	TOB2	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	350	290	1.2069	
133	TOB1	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	350	290	1.2069	
134	DAB2IP	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	350	290	1.2069	
135	CPEB4	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	350	290	1.2069	
136	CPEB3	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	350	290	1.2069	
137	RASAL2	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	350	290	1.2069	
138	PPP2CA	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	194.372	234.204	1.20493	
139	APBA1	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [source:swissprot;acc:q02410]	271.752	225.68	1.20415	
140	RRAGA	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	59	49	1.20408	
141	RRAGC	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	59	49	1.20408	
142	RRAGB	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	59	49	1.20408	
143	ANLN	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	59	49	1.20408	
144	KCNIP1	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	265.686	319.651	1.20312	
145	KCNIP4	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	265.639	319.546	1.20293	
146	KCNIP2	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [source:refseq;acc:nm_173193]	265.632	319.531	1.20291	
147		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	50.7983	42.3003	1.2009	
148	UNC84A	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	296.677	247.559	1.19841	
149		atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	142	170	1.19718	
150	MYO5B	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	55	46	1.19565	
151	MYO5C	myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]	55	46	1.19565	
152		myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	55	46	1.19565	
153	RBM15B	chromosome 3p21.1 gene sequence. [source:refseq;acc:nm_013286]	249.663	298.263	1.19466	
154	RGS19	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [source:swissprot;acc:p49795]	249.663	298.263	1.19466	
155	RBM15	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [source:swissprot;acc:q96t37]	249.663	298.263	1.19466	
156	RGS20	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [source:swissprot;acc:o76081]	249.663	298.263	1.19466	
157	LBX1	transcription factor lbx1. [source:swissprot;acc:p52954]	249.663	298.263	1.19466	
158	GPSM2	mosaic protein lgn. [source:swissprot;acc:p81274]	249.663	298.263	1.19466	
159	RGS17	regulator of g-protein signaling 17 (rgs17). [source:swissprot;acc:q9ugc6]	249.663	298.263	1.19466	
160	GNAO1	guanine nucleotide-binding protein g(o), alpha subunit 1. [source:swissprot;acc:p09471]	249.663	298.263	1.19466	
161	RAP1GAP	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	249.663	298.263	1.19466	
162	NOSTRIN	nostrin. [source:refseq;acc:nm_052946]	209.299	249.187	1.19058	
163	SNF8	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	209.299	249.187	1.19058	
164	SLC39A6	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	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]	209.299	249.187	1.19058	
166	NAPG	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	209.299	249.187	1.19058	
167	GAD1	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	209.299	249.187	1.19058	
168		gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	82.5916	98.0548	1.18722	
169	ATG3	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	82.5916	98.0548	1.18722	
170	TIA1	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	227.199	192.715	1.17894	
171	TIAL1	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	227.202	192.823	1.17829	
172	TIPRL	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [source:refseq;acc:nm_152902]	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]	227.032	193.056	1.17599	
174	DGCR14	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	335	286	1.17133	
175	COPS3	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	199.949	234.187	1.17123	
176	POLE4	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	275.754	235.908	1.1689	

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/