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.

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

Results: HTML CSV LaTeX

Showing element 2513 to 2562 of 66312 in total

Filtered  : 1

Rank	description	Network Comparison Type	Value Type	Interaction Map	red	green	network_comparison
158	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Divided	Rooted	High confidence	56.3507	66.1252	1.17346
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Subtracted	Ranked		312	284	28
	dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937]	Divided		Low confidence	219.838	207.417	1.05988
	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4]	Subtracted	Squared	High confidence	76360.8	58841.7	17519.1
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Divided	Measured		23693.7	18263	1.29736
	mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749]			Low confidence	6434.71	6976.28	1.08416
	mosaic protein lgn. [swissprot;acc:p81274]		Ranked	High confidence	249.663	298.263	1.19466
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Subtracted	Measured		9035	7279.6	1755.4
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]		Rooted		149.397	136.972	12.425
	proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591]		Ranked	Low confidence	216.796	205.073	11.723
	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]		Rooted		65.9882	70.626	4.6378
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	Divided	Squared	High confidence	89182.8	125229	1.40418
	spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470]	Subtracted		Low confidence	53603.3	47680.8	5922.5
	striatin. [swissprot;acc:o43815]	Divided	Rooted		66.4354	70.987	1.06851
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Subtracted	Measured		10491.4	9831.19	660.21
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Divided	Squared		57732.3	51372.1	1.12381
159	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (6pf-2-k/fru- 2,6-p2ase brain/placenta-type isozyme) (ipfk-2) [includes: 6- phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:q16875]	Subtracted			53380.6	47490	5890.6
	60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914]		Ranked		216.79	205.07	11.72
	brain protein 44. [swissprot;acc:o95563]	Divided	Measured		10392.1	11259.7	1.08349
	c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835]		Ranked		219.838	207.417	1.05988
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Subtracted		High confidence	312	284	28
	histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773]	Divided	Squared	Low confidence	22187.9	19810.5	1.12001
	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	Subtracted		High confidence	76296.4	58801.6	17494.8
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]		Measured		9035	7279.6	1755.4
	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]		Rooted	Low confidence	62.9048	67.5424	4.6376
	necdin. [swissprot;acc:q99608]	Divided	Measured	High confidence	23693.7	18263	1.29736
	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]		Ranked		249.663	298.263	1.19466
	rna-binding protein. [refseq;acc:nm_019027]		Rooted		52.7642	61.9019	1.17318
	septin 6. [swissprot;acc:q14141]		Squared		88953.6	124854	1.40359
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	Subtracted	Measured	Low confidence	4900.7	5555.81	655.11
	transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802]	Divided	Rooted		65.5823	70.0536	1.06818
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Subtracted		High confidence	113.983	101.979	12.004
160	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (6pf-2-k/fru- 2,6-p2ase liver isozyme) [includes: 6-phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:p16118]		Squared	Low confidence	53380.6	47490	5890.6
	adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054]	Divided	Ranked		222.31	235.538	1.0595
	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]		Rooted	High confidence	52.7642	61.9019	1.17318
	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Subtracted		Low confidence	64.1512	68.7584	4.6072
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]		Measured	High confidence	9035	7279.6	1755.4
	guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]	Divided	Ranked		249.663	298.263	1.19466
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Squared		173408	242989	1.40126
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Subtracted	Rooted		43.4291	31.7159	11.7132
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Divided	Measured		23693.7	18263	1.29736
	methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898]			Low confidence	10452.8	11320.8	1.08304
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Subtracted	Ranked	High confidence	312	284	28
	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Divided	Squared	Low confidence	54208.6	48413.8	1.11969
	proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332]	Subtracted	Ranked		216.783	205.066	11.717
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Divided	Rooted		65.7817	70.2555	1.06801
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Subtracted	Measured		7013	7662.77	649.77
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]		Squared	High confidence	42788.3	60162.6	17374.3
161	adenomatous polyposis coli like. [refseq;acc:nm_005883]	Divided	Ranked	Low confidence	222.34	235.547	1.0594
	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	Subtracted	Rooted		64.1536	68.7605	4.6069

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.