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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 551 to 600 of 7460 in total

Interaction Map

: High confidence
Value Type

: Ranked

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

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/