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 551 to 600 of 7460 in total

Value Type

: Ranked
Interaction Map

: High confidence

Rank	description	Network Comparison Type	Filtered	red	green	network_comparison
138	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Divided	1	194.372	234.204	1.20493
138	serpin b11. [swissprot;acc:q96p15]	Subtracted	0	16853	15123	1730
139	alpha crystallin a chain. [swissprot;acc:p02489]	Divided	0	16372.4	13972.2	1.17178
	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). [swissprot;acc:q02410]	Divided	1	271.752	225.68	1.20415
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Subtracted	1	287.41	256.835	30.575
	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]		0	16853	15123	1730
140	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]		1	228.306	198.011	30.295
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]		0	15081.8	16802.1	1720.3
	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). [swissprot;acc:o60476]	Divided	0	16411.9	14027.1	1.17001
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Divided	1	59	49	1.20408
141	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Subtracted	1	239.991	269.238	29.247
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Divided	0	7690.02	8991.19	1.1692
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Divided	1	59	49	1.20408
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Subtracted	0	9411.34	11119.7	1708.36
142	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Divided	1	59	49	1.20408
	thrombospondin 3 precursor. [swissprot;acc:p49746]	Subtracted	1	239.99	269.234	29.244
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Subtracted	0	16614	18296	1682
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Divided	0	8214.41	7026.41	1.16908
143	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]		1	59	49	1.20408
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]		0	11124.8	13005.3	1.16904
	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	Subtracted	0	9545	7868	1677
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]		1	240.133	211.382	28.751
144	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]		1	239.35	267.915	28.565
	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Divided	0	11123.4	13000.1	1.16872
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Divided	1	265.686	319.651	1.20312
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Subtracted	0	12225.7	13893.1	1667.4
145	lamin b2. [swissprot;acc:q03252]		0	12135.4	13802	1666.6
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]		1	239.336	267.881	28.545
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Divided	1	265.639	319.546	1.20293
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]		0	7955.61	6817.49	1.16694
146	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]		0	12577.8	14662.1	1.16571
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]		1	265.632	319.531	1.20291
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	0	3208.8	4871.6	1662.8
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Subtracted	1	239.336	267.879	28.543
147	60s ribosomal protein l7. [swissprot;acc:p18124]	Divided	0	11080.3	9505.89	1.16562
	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	Subtracted	1	239.32	267.842	28.522
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Divided	1	50.7983	42.3003	1.2009
	tubby protein homolog. [swissprot;acc:p50607]	Subtracted	0	12303.7	10641.7	1662
148	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]		0	7706.5	6058	1648.5
	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. [refseq;acc:nm_001457]		1	226.582	198.444	28.138
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Divided	1	296.677	247.559	1.19841
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]		0	6755.71	7863.63	1.164
149	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]		1	142	170	1.19718
	block 23. [sptrembl;acc:q8nhw5]		0	11469.3	13334.8	1.16265
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Subtracted	0	13942.8	15586.4	1643.6
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]		1	226.582	198.444	28.138
150	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513]		0	7495.26	9130.38	1635.12
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Divided	1	55	46	1.19565
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Subtracted	1	226.582	198.444	28.138
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Divided	0	8730	7516	1.16152

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/