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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 3228 in total

Hugo  : no value
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1

red	Rank	green	description	network_comparison
0.00001	2756	0.00001	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	1
	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]
15	2	28	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]	1.86667
50.7983	147	42.3003	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	1.2009
55	152	46	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	1.19565
82.5916	168	98.0548	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	1.18722
88.2482	85	110.265	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	1.24949
	88		hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
	94		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
	99		melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
112	215	126	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	1.125
	221		myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
129.219	566	121.261	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	1.06563

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.