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.

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 3228 in total

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

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