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.

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

Results: HTML CSV LaTeX

Showing element 101 to 150 of 473 in total

Network Comparison Type  : Subtracted
Value Type  : Ranked
Interaction Map  : High confidence
red  : 0
Filtered  : 1
network_comparison  : 0
green  : 0

Rank	description
2856	high mobility group protein 2 (hmg-2). [swissprot;acc:p26583]
2857	protein kinase c, delta type (ec 2.7.1.-) (npkc-delta). [swissprot;acc:q05655]
2858	tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [swissprot;acc:p34925]
2859	homeobox protein nkx-6.1. [swissprot;acc:p78426]
2860	importin 9. [refseq;acc:nm_018085]
2861	glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]
2862	syndecan-3 (synd3). [swissprot;acc:o75056]
2863	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
2864	mago nashi protein homolog. [swissprot;acc:p50606]
2865	t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542]
2866	syntaxin 5. [swissprot;acc:q13190]
2867	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
2868	eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [swissprot;acc:p04765]
2869	phosphoribosyl pyrophosphate synthetase-associated protein 1 (prpp synthetase-associated protein 1) (39 kda phosphoribosypyrophosphate synthetase-associated protein) (pap39). [swissprot;acc:q14558]
2870	adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979]
2871	vps28 protein homolog. [swissprot;acc:q9uk41]
2872	transcriptional repressor nac1. [refseq;acc:nm_052876]
2873	integrin beta-2 precursor (cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta-subunit) (cd18) (complement receptor c3 beta- subunit). [swissprot;acc:p05107]
2874	protein c21orf2 (c21orf-humf09g8.5) (yf5/a2). [swissprot;acc:o43822]
2875	alpha crystallin a chain. [swissprot;acc:p02489]
2876	high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [swissprot;acc:o76083]
2877	runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196]
2878	nadh-ubiquinone oxidoreductase 49 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-49kd) (ci-49kd). [swissprot;acc:o75306]
2879	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]
2880	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]
2881	collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [refseq;acc:nm_130386]
2882	xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [swissprot;acc:p47989]
2883	pantothenate kinase 4 (ec 2.7.1.33) (pantothenic acid kinase 4) (hpank4). [swissprot;acc:q9nve7]
2884	peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [swissprot;acc:q9hbh1]
2885	carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786]
2886	complement component c8 alpha chain precursor. [swissprot;acc:p07357]
2887	mothers against decapentaplegic homolog interacting protein (madh-interacting protein) (smad anchor for receptor activation) (receptor activation anchor) (hsara) (novel serine protease) (nsp). [swissprot;acc:o95405]
2888	eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [swissprot;acc:q14240]
2889	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]
2890	ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [swissprot;acc:q9uff9]
2891	putative mitochondrial solute carrier; hypothetical protein npd016; putative mitochondrial solute carrier. [refseq;acc:nm_031212]
2892	cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [refseq;acc:nm_015076]
2893	atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [swissprot;acc:p18859]
2894	transcription initiation factor iie, alpha subunit (tfiie-alpha) (general transcription factor iie 56 kda subunit). [swissprot;acc:p29083]
2895	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]
2896	bone morphogenetic protein 6 precursor (bmp-6). [swissprot;acc:p22004]
2897	serine/threonine kinase 38 like. [refseq;acc:nm_015000]
2898	likely ortholog of mouse c-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; c-type lectin 13; likely ortholog of rat kupffer cell c-type lectin receptor. [refseq;acc:nm_173535]
2899	sparc-like protein 1 precursor (high endothelial venule protein) (hevin) (mast 9). [swissprot;acc:q14515]
2900	schwannomin interacting protein 1. [refseq;acc:nm_014575]
2901	casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4]
2902	ubiquitin protein ligase. [refseq;acc:nm_130466]
2903	protein transport protein sec24d (sec24-related protein d). [swissprot;acc:o94855]
2904	6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393]
2905	integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [swissprot;acc:p05556]

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.