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

Results: HTML CSV LaTeX

Showing element 614 to 663 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
77	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]	Measured	1	4612.39	3093.6	1.49095
	tigger transposable element derived 6. [refseq;acc:nm_030953]	Rooted	0	13.0605	17.6725	1.35313
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	Ranked	1	254.692	202.668	1.2567
78	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Squared		117858	70570.1	1.67008
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Measured		4800.81	7132.71	1.48573
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Measured	0	161	95	1.69474
	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	Ranked		7584.72	9706.12	1.27969
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	Rooted		13.0525	17.6565	1.35273
	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	Squared		0.213018	0.591716	2.77777
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Rooted	1	63.7477	48.1589	1.3237
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Ranked	1	254.693	202.668	1.2567
79	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Ranked	0	9465.55	12106.5	1.27901
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Squared		396.995	1088.19	2.74107
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	Measured		323.79	544.991	1.68316
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Measured	1	3074.57	4567.51	1.48558
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Squared		117850	70566.8	1.67005
	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]	Rooted		63.7477	48.1588	1.3237
	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	Rooted	0	13.0522	17.6559	1.35271
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Ranked	1	254.693	202.668	1.2567
80	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	Rooted	0	44.2946	32.7593	1.35212
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Ranked	0	9102.34	11617.9	1.27636
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Measured	1	4133.47	5945.32	1.43834
	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	Measured	0	293	493	1.68259
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	Squared	0	955.08	2589.83	2.71164
	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]	Rooted	1	63.7477	48.1594	1.32368
	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]	Squared		117718	70505.9	1.66962
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Ranked		254.691	202.668	1.25669
81	cyclin g2. [swissprot;acc:q16589]	Squared		117718	70505.9	1.66962
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Rooted	0	54.2583	40.2058	1.34951
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Measured	1	4136.36	5943.56	1.43691
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	Squared	0	45.9662	123.721	2.69156
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Ranked	0	14463	11356	1.2736
	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]	Rooted	1	63.7475	48.1615	1.32362
	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	Measured	0	30	50	1.66667
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Ranked	1	254.614	202.646	1.25645
82	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	Squared	0	374.181	141.849	2.63788
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Rooted	1	60.8022	79.5099	1.30768
	cyclin g1 (cyclin g). [swissprot;acc:p51959]	Squared	1	117718	70505.8	1.66962
	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	Ranked	0	7706.5	6058	1.27212
	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Ranked	1	267.636	335.359	1.25304
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Measured	0	191.333	115.333	1.65896
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Measured	1	4172.91	5954.48	1.42694
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	Rooted	0	10.9527	8.13999	1.34554
83	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	Rooted		10.9038	8.12243	1.34243
	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	Measured		166.114	100.887	1.64654
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Ranked	1	88.2482	110.265	1.24949
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Measured		4932.27	7033.29	1.42597
	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]	Squared		117718	70505.9	1.66962
	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]	Rooted		63.6507	48.7127	1.30666
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Ranked	0	18359.8	14447.8	1.27077

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/