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

Results: HTML CSV LaTeX

Showing element 2580 to 2629 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	red	green	network_comparison
645	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	Rooted	63.1463	68.1044	1.07852
646	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	Squared	27898	32866.2	1.17808
	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]	Rooted	63.1463	68.1044	1.07852
	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]	Measured	4019.88	4522.61	1.12506
	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	Ranked	216.731	229.549	1.05914
647	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	Rooted	64.5657	69.6237	1.07834
	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	Squared	33384.2	39324.9	1.17795
	dynein light chain 2. [refseq;acc:nm_080677]	Ranked	216.731	229.549	1.05914
	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Measured	5167.88	4594.43	1.12481
648	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	Ranked	218.227	206.078	1.05895
	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	Squared	29174	34363.5	1.17788
	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	Measured	5248.07	5901.72	1.12455
	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	Rooted	64.5685	69.6269	1.07834
649	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	Ranked	233.725	220.751	1.05877
	grancalcin. [swissprot;acc:p28676]	Rooted	64.5659	69.624	1.07834
	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	Squared	29173.8	34362.7	1.17786
	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]	Measured	5248.07	5901.72	1.12455
650	chromodomain y-like protein 2. [refseq;acc:nm_152342]	Squared	29016.1	34169.2	1.17759
	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530]	Measured	8362.81	9402.7	1.12435
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Rooted	64.566	69.6241	1.07834
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Ranked	228.986	216.276	1.05877
651	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]		233.725	220.751
	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	Measured	5168.43	4597.44	1.1242
	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	Rooted	64.5685	69.6269	1.07834
	testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]	Squared	29012.2	34163.9	1.17757
652	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	Rooted	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
	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	Measured	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
	dok-like protein. [refseq;acc:nm_024872]	Ranked	216.504	204.622	1.05807
	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	Measured	5560.06	6248.27	1.12378
	testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]	Squared	29012.4	34164	1.17757
654	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Ranked	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
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	Squared	27174.1	31992.4	1.17731
655	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	Measured	4088.63	4593.43	1.12346
	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	Ranked	216.504	204.622	1.05807
	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]	Rooted	59.9021	64.5838	1.07816
	sprouty homolog 3 (spry-3). [swissprot;acc:o43610]	Squared	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
	single-minded homolog 1. [swissprot;acc:p81133]	Rooted	59.9021	64.5838	1.07816
	sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]	Squared	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	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Measured	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	apical-like protein (apxl protein). [swissprot;acc:q13796]	Measured	6088.77	6834.87	1.12254

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.