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

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Showing element 1 to 50 of 3228 in total

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

Hugo	description	Rank
no value	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	2756
	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]	2802
	60s ribosomal protein l37a. [swissprot;acc:p12751]	2959
	calmodulin. [swissprot;acc:p02593]	2928
	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	3226
	gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [swissprot;acc:p13284]	3101
	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	2989
	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	2863
	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	2767
	histone h2a.e (h2a/e). [swissprot;acc:q99878]	2765
	importin 9. [refseq;acc:nm_018085]	2860
	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]	3044
	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]	2880
	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]	2825
	muts protein homolog 5. [swissprot;acc:o43196]	3148
	nanos (fragment). [sptrembl;acc:q8wy41]	2803
	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	3080
	peregrin (bromodomain and phd finger-containing protein 1) (br140 protein). [swissprot;acc:p55201]	2820
	placental protein 11 precursor (ec 3.4.21.-) (pp11). [swissprot;acc:p21128]	3076
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	3100
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	2910
	ptd016 protein. [refseq;acc:nm_016125]	3093
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	3119
	retinoic acid receptor rxr-beta. [swissprot;acc:p28702]	3067
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	2895
	serine/threonine kinase 38 like. [refseq;acc:nm_015000]	2897
	serine/threonine protein kinase mask; ste20-like kinase mst4. [refseq;acc:nm_016542]	2982
	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]	2867
	skeletal muscle and kidney enriched inositol phosphatase isoform 1; 43-kda form skeletal muscle and kidney enriched inositol phosphatase. [refseq;acc:nm_016532]	2994
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	3038
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	2879
	suppressor of actin 1. [refseq;acc:nm_014016]	2826
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	2940
	transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3]	2790
	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	3178
	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]	2828
	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	2819
	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]	3086
	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	2793
ACVR1	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]	3050
ACVRL1	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]	2952
AKAP5	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]	2788
ALDH1L1	10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	2922
ALDH3A2	fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [swissprot;acc:p51648]	3181
ALDH3B1	aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353]	3222
ALDH3B2	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	2992
ALDOA	fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075]	2907
ALDOB	fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062]	2973
ALDOC	fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [swissprot;acc:p09972]	3087
AOX1	aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278]	2960

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.