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

Results: HTML CSV LaTeX

Showing element 5208 to 5257 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
651	vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050]	Squared	Subtracted	26032.5	30417.7	4385.2
652	atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632]			26030.5	30415.2	4384.7
	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	Rooted	Divided	64.5672	69.6254	1.07834
	chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]	Squared		29012.2	34163.9	1.17757
	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	Ranked	Subtracted	214.256	202.139	12.117
	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	Measured		6456.35	7169.75	713.4
	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	Rooted		49.7435	45.0586	4.6849
	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	Measured	Divided	5168.43	4597.44	1.1242
	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	Ranked		248.994	235.255	1.0584
653	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	Rooted		64.4927	69.539	1.07825
	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388]	Measured	Subtracted	6441.17	7154.55	713.38
	dok-like protein. [refseq;acc:nm_024872]	Ranked	Divided	216.504	204.622	1.05807
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]		Subtracted	214.256	202.139	12.117
	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Rooted		49.7435	45.0586	4.6849
	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	Measured	Divided	5560.06	6248.27	1.12378
	testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]	Squared		29012.4	34164	1.17757
	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487]		Subtracted	26029.8	30414.4	4384.6
654	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Ranked	Divided	216.504	204.622	1.05807
	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	Measured		4088.63	4593.43	1.12346
	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]	Rooted		59.9021	64.5838	1.07816
			Subtracted			4.6817
	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]	Ranked		214.256	202.139	12.117
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	Squared	Divided	27174.1	31992.4	1.17731
	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	Measured	Subtracted	6455.66	7168.82	713.16
	vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488]	Squared		26029.1	30413.6	4384.5
655	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	Measured	Divided	4088.63	4593.43	1.12346
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]		Subtracted	6441.14	7154.13	712.99
	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	Ranked	Divided	216.504	204.622	1.05807
	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]		Subtracted	214.256	202.14	12.116
	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]	Rooted	Divided	59.9021	64.5838	1.07816
			Subtracted			4.6817
	musashi 2 isoform a. [refseq;acc:nm_138962]	Squared		15569.5	19953.6	4384.1
	sprouty homolog 3 (spry-3). [swissprot;acc:o43610]		Divided	27174.1	31992.4	1.17731
656	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	Measured		6139.04	6893.7	1.12293
	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]	Ranked	Subtracted	214.256	202.14	12.116
	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	Measured		6455.02	7167.96	712.94
	musashi 1. [refseq;acc:nm_002442]	Squared		15569.5	19953.6	4384.1
	single-minded homolog 1. [swissprot;acc:p81133]	Rooted	Divided	59.9021	64.5838	1.07816
			Subtracted			4.6817
	sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]	Squared	Divided	27174.1	31992.4	1.17731
	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Ranked		216.504	204.622	1.05807
657	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366]	Measured	Subtracted	10341.2	9630.35	710.85
	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]	Ranked		214.256	202.14	12.116
	nuclear protein ukp68. [refseq;acc:nm_024824]	Squared		15569.5	19953.6	4384.1
	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	Rooted		63.1365	67.8053	4.6688
	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Measured	Divided	6079.26	6824.47	1.12258
	sprouty homolog 2 (spry-2). [swissprot;acc:o43597]	Squared		27174.1	31992.4	1.17731
	synapsin iii. [swissprot;acc:o14994]	Ranked		229.072	216.576	1.0577
	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	Rooted		64.75	69.8065	1.07809
658	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]		Subtracted	50.3345	45.6718	4.6627

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.