Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 601 to 650 of 14920 in total

Interaction Map

: High confidence
Network Comparison Type

: Divided

Rank	Value Type	Filtered	description	red	network_comparison	green
76	Measured	0	dead-box protein. [refseq;acc:nm_018665]	313.667	1.71403	183
	Measured	1	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	4599.26	1.50373	3058.57
	Ranked	0	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	3474	1.28905	2695
	Ranked	1	db83 protein. [swissprot;acc:p57088]	288	1.25694	362
	Squared	0	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	20.3193	2.83112	57.5264
	Squared	1	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	110342	1.67024	184298
	Rooted	0	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	10.025	1.35766	13.6105
	Rooted	1	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	27.9136	1.33581	37.2872
77	Measured	0	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	712.071	1.70956	416.524
	Measured	1	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	4612.39	1.49095	3093.6
	Ranked	0	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	8821.32	1.28853	11366.5
	Ranked	1	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	254.692	1.2567	202.668
	Squared	0	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897]	328.83	2.79146	917.917
	Squared	1	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	110342	1.67024	184298
	Rooted	0	tigger transposable element derived 6. [refseq;acc:nm_030953]	13.0605	1.35313	17.6725
	Rooted	1	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	39.9725	1.32584	52.9973
78	Measured	0	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	161	1.69474	95
	Measured	1	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	4800.81	1.48573	7132.71
	Ranked	0	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	7584.72	1.27969	9706.12
	Ranked	1	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	254.693	1.2567	202.668
	Squared	0	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	0.213018	2.77777	0.591716
	Squared	1	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	117858	1.67008	70570.1
	Rooted	0	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	13.0525	1.35273	17.6565
	Rooted	1	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	63.7477	1.3237	48.1589
79	Measured	0	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	323.79	1.68316	544.991
	Measured	1	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	3074.57	1.48558	4567.51
	Ranked	0	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	9465.55	1.27901	12106.5
	Ranked	1	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	254.693	1.2567	202.668
	Squared	0	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	396.995	2.74107	1088.19
	Squared	1	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	117850	1.67005	70566.8
	Rooted	0	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	13.0522	1.35271	17.6559
	Rooted	1	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	63.7477	1.3237	48.1588
80	Measured	0	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	293	1.68259	493
	Measured	1	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	4133.47	1.43834	5945.32
	Ranked	0	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	9102.34	1.27636	11617.9
	Ranked	1	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	254.691	1.25669	202.668
	Squared	0	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	955.08	2.71164	2589.83
	Squared	1	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	117718	1.66962	70505.9
	Rooted	0	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	44.2946	1.35212	32.7593
	Rooted	1	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	63.7477	1.32368	48.1594
81	Measured	0	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	30	1.66667	50
	Measured	1	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	4136.36	1.43691	5943.56
	Ranked	0	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	14463	1.2736	11356
	Ranked	1	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	254.614	1.25645	202.646
	Squared	0	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	45.9662	2.69156	123.721
	Squared	1	cyclin g2. [swissprot;acc:q16589]	117718	1.66962	70505.9
	Rooted	0	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	54.2583	1.34951	40.2058
	Rooted	1	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	63.7475	1.32362	48.1615
82	Measured	0	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	191.333	1.65896	115.333
82	Measured	1	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	4172.91	1.42694	5954.48

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.

- http://analysis.yellowcouch.org/