MK5 Microarray Data

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 5908 to 5957 of 29840 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

red	Value Type	Rank	description	green	network_comparison	Filtered
201.37	Ranked	2651	nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221]	201.594	1.00111	1
201.445		2655	b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749]	201.667	1.0011
201.451		2652	nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838]	201.673
201.452		2653	nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653]	201.674
		2654	nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653]
201.476		2744	transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354]	201.514	1.00019
		2745	frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331]
		2746	transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478]
201.477		2747	bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263]		1.00018
201.478		202	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	228.784	1.13553
201.515		203	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	228.752	1.13516
		204	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
201.652		2696	iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399]	201.794	1.0007
201.949		28	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	153.671	1.31416
201.96		2521	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	201.488	1.00234
		2523	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]
		2524	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]
		2526	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
202.027		979	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	195.386	1.03399
202.123		2729	ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670]	202.06	1.00031
202.142		2598	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542]	202.436	1.00145
202.156	Measured	47	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	438.016	2.16672	0
202.163		46	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	438.035	2.16674
202.211	Ranked	1918	endothelial-derived gene 1. [refseq;acc:nm_025205]	200.18	1.01015	1
202.229		2733	p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831]	202.172	1.00028
202.233		2732	general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830]	202.175	1.00029
202.312		2268	tripartite motif protein 2. [swissprot;acc:q9c040]	203.437	1.00556
202.358		1636	beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457]	199.408	1.01479
		1637	26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210]
202.366		2255	alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911]	203.57	1.00595
202.374	Measured	45	tigger transposable element derived 6. [refseq;acc:nm_030953]	438.605	2.1673	0
202.386	Ranked	1823	fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116]	200.086	1.0115	1
		1825	fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114]
202.393		1826	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	200.094	1.01149
202.395		2560	monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283]	202.042	1.00175
202.41		1828	fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787]	200.115	1.01147
202.414		2233	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382]	203.691	1.00631
202.436	Squared	419	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	212.386	1.04915	0
202.821	Ranked	2614	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206]	202.54	1.00139	1
		2615	transcription factor relb (i-rel). [swissprot;acc:q01201]
		2616	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]
		2617	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]
203.071		1864	fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281]	200.89	1.01086
		1867	multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155]
203.151		2674	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	202.948	1.001
203.353		2366	14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	202.529	1.00407
203.381		991	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762]	196.76	1.03365
203.592		2681	ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112]	203.787	1.00096
203.673	Rooted	301	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]	182.638	1.11517
		302	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]

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.