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

Results: HTML CSV LaTeX

Showing element 273 to 322 of 3730 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
137	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [source:swissprot;acc:q9hbi6]	0	12328.5	10501	1.17403	
137	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	1	350	290	1.2069	
138	likely ortholog of rat cytochrome p450 4x1. [source:refseq;acc:nm_178033]	0	12384.7	10549.4	1.17397	
138	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]	1	194.372	234.204	1.20493	
139	alpha crystallin a chain. [source:swissprot;acc:p02489]	0	16372.4	13972.2	1.17178	
139	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]	1	271.752	225.68	1.20415	
140	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	0	16411.9	14027.1	1.17001	
140	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	1	59	49	1.20408	
141	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	0	7690.02	8991.19	1.1692	
141	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	1	59	49	1.20408	
142	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	1	59	49	1.20408	
142	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	0	8214.41	7026.41	1.16908	
143	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	1	59	49	1.20408	
143	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source:refseq;acc:nm_032959]	0	11124.8	13005.3	1.16904	
144	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source:refseq;acc:nm_145325]	0	11123.4	13000.1	1.16872	
144	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	1	265.686	319.651	1.20312	
145	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	1	265.639	319.546	1.20293	
145	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	0	7955.61	6817.49	1.16694	
146	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	0	12577.8	14662.1	1.16571	
146	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]	1	265.632	319.531	1.20291	
147	60s ribosomal protein l7. [source:swissprot;acc:p18124]	0	11080.3	9505.89	1.16562	
147	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	1	50.7983	42.3003	1.2009	
148	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	1	296.677	247.559	1.19841	
148	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	0	6755.71	7863.63	1.164	
149	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	1	142	170	1.19718	
149	block 23. [source:sptrembl;acc:q8nhw5]	0	11469.3	13334.8	1.16265	
150	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	1	55	46	1.19565	
150	zinc finger protein-like 1; zinc-finger protein in men1 region. [source:refseq;acc:nm_006782]	0	8730	7516	1.16152	
151	myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]	1	55	46	1.19565	
151	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [source:swissprot;acc:q15695]	0	7502.08	6461.83	1.16098	
152	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	1	55	46	1.19565	
152	similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	0	11438	13277.1	1.16079	
153	chromosome 3p21.1 gene sequence. [source:refseq;acc:nm_013286]	1	249.663	298.263	1.19466	
153	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [source:swissprot;acc:p23258]	0	7879.3	6789.92	1.16044	
154	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	0	10883	12622.8	1.15986	
154	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [source:swissprot;acc:p49795]	1	249.663	298.263	1.19466	
155	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [source:refseq;acc:nm_138393]	0	12759.4	11028.8	1.15692	
155	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [source:swissprot;acc:q96t37]	1	249.663	298.263	1.19466	
156	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]	1	249.663	298.263	1.19466	
156	tubby protein homolog. [source:swissprot;acc:p50607]	0	12303.7	10641.7	1.15618	
157	transcription factor lbx1. [source:swissprot;acc:p52954]	1	249.663	298.263	1.19466	
157	transcription initiation factor iie, beta subunit (tfiie-beta). [source:swissprot;acc:p29084]	0	18079	15652	1.15506	
158	mosaic protein lgn. [source:swissprot;acc:p81274]	1	249.663	298.263	1.19466	
158	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	0	10060.2	11616.4	1.15469	
159	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	0	5813.32	6706.32	1.15361	
159	regulator of g-protein signaling 17 (rgs17). [source:swissprot;acc:q9ugc6]	1	249.663	298.263	1.19466	
160	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [source:swissprot;acc:q9uiv1]	0	11732	13530.6	1.15331	
160	guanine nucleotide-binding protein g(o), alpha subunit 1. [source:swissprot;acc:p09471]	1	249.663	298.263	1.19466	
161	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	0	5781.93	6660.63	1.15197	
161	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	1	249.663	298.263	1.19466	

Legend:
- Rank is the rank after comparing the two networks
- 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/