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

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Showing element 1 to 50 of 3228 in total

red  : 0.00001
green  : 0.00001
Value Type  : Ranked
Network Comparison Type  : Divided
network_comparison  : 1
Interaction Map  : High confidence
Filtered  : 1

Hugo	Rank	description
no value	2756	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]
	2765	histone h2a.e (h2a/e). [swissprot;acc:q99878]
	2767	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
	2790	transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3]
	2793	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]
	2802	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060]
	2803	nanos (fragment). [sptrembl;acc:q8wy41]
	2819	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]
	2820	peregrin (bromodomain and phd finger-containing protein 1) (br140 protein). [swissprot;acc:p55201]
	2825	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
	2826	suppressor of actin 1. [refseq;acc:nm_014016]
	2828	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]
	2860	importin 9. [refseq;acc:nm_018085]
	2863	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
	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]
	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]
	2895	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]
	2897	serine/threonine kinase 38 like. [refseq;acc:nm_015000]
	2910	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]
	2928	calmodulin. [swissprot;acc:p02593]
	2940	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]
	2959	60s ribosomal protein l37a. [swissprot;acc:p12751]
	2982	serine/threonine protein kinase mask; ste20-like kinase mst4. [refseq;acc:nm_016542]
	2989	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]
	2994	skeletal muscle and kidney enriched inositol phosphatase isoform 1; 43-kda form skeletal muscle and kidney enriched inositol phosphatase. [refseq;acc:nm_016532]
	3038	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]
	3044	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]
	3067	retinoic acid receptor rxr-beta. [swissprot;acc:p28702]
	3076	placental protein 11 precursor (ec 3.4.21.-) (pp11). [swissprot;acc:p21128]
	3080	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]
	3086	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]
	3093	ptd016 protein. [refseq;acc:nm_016125]
	3100	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]
	3101	gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [swissprot;acc:p13284]
	3119	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]
	3148	muts protein homolog 5. [swissprot;acc:o43196]
	3178	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]
	3226	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]
ACVR1	3050	activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771]
ACVRL1	2952	serine/threonine-protein kinase receptor r3 precursor (ec 2.7.1.37) (skr3) (activin receptor-like kinase 1) (alk-1) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:p37023]
AKAP5	2788	a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588]
ALDH1L1	2922	10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]
ALDH3A2	3181	fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [swissprot;acc:p51648]
ALDH3B1	3222	aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353]
ALDH3B2	2992	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]
ALDOA	2907	fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075]
ALDOB	2973	fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062]
ALDOC	3087	fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [swissprot;acc:p09972]
AOX1	2960	aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278]

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
- Hugo is the HGNC identifier if it exists
- 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.