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 1530 to 1579 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
96	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Rooted	Subtracted	0	27.4843	22.4483	5.036
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Rooted	Divided	1	47.6504	36.9304	1.29028
	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	Measured	Subtracted		16177.9	19235.4	3057.5
		Squared	Subtracted		90226	126939	36713
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Measured	Divided	0	154	0.00001	15400000
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Rooted	Divided		65.4535	49.8523	1.31295
	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	Ranked	Subtracted		11523	13685.4	2162.4
97	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	Measured	Divided		728.65	476.619	1.52879
	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	Measured	Divided	1	2820.51	3897.1	1.3817
		Ranked	Subtracted		271.752	225.68	46.072
	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Squared	Divided		227160	146079	1.55505
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Squared	Subtracted		126408	89940.5	36467.5
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	Rooted			40.2797	24.3705	15.9092
	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	Squared		0	6188.69	7568.12	1379.43
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Ranked	Divided	1	88.2482	110.265	1.24949
	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	Ranked		0	8335.82	10228.3	1.22703
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Squared			10489.8	23426.5	2.23326
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Measured	Subtracted		111.278	434.911	323.633
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Rooted	Subtracted		22.2259	17.2182	5.0077
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]		Divided	1	47.6504	36.9304	1.29028
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]		Divided	0	13.2903	17.4395	1.3122
	septin 10 isoform 1. [refseq;acc:nm_144710]	Measured	Subtracted	1	16067.4	19094.4	3027
	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	Ranked		0	11522.8	13684.9	2162.1
98	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Rooted		0	83.9673	88.8829	4.9156
	brain protein 44. [swissprot;acc:o95563]	Measured		1	15999.1	19007.1	3008
	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	Rooted		1	40.2797	24.3705	15.9092
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Measured		0	39165	39485	320
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Ranked	Divided	1	88.2482	110.265	1.24949
	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	Squared	Subtracted	0	310884	312261	1377
	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	Ranked	Divided		7234.6	8858.94	1.22452
	pp3111 protein. [refseq;acc:nm_022156]	Measured			789	530	1.48868
	pp3111 protein. [refseq;acc:nm_022156]	Squared			147.342	66.4852	2.21616
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Measured		1	2353.63	3225.65	1.3705
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Ranked	Subtracted		204.641	160.957	43.684
	septin 10 isoform 1. [refseq;acc:nm_144710]	Squared	Subtracted		89578.7	125883	36304.3
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	Rooted	Divided	0	13.2903	17.4395	1.3122
	transcription factor lbx1. [swissprot;acc:p52954]	Rooted		1	47.6504	36.9304	1.29028
	trs85 homolog. [swissprot;acc:q9y2l5]	Squared		1	227160	146079	1.55505
	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	Ranked	Subtracted	0	11520.7	13680.4	2159.7
99	brain protein 44. [swissprot;acc:o95563]	Squared		1	89182.8	125229	36046.2
	dystrophin. [swissprot;acc:p11532]	Measured		0	427.217	111.739	315.478
	jun dimerization protein. [refseq;acc:nm_130469]	Ranked		1	204.641	160.957	43.684
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Ranked	Divided		88.2482	110.265	1.24949
	mosaic protein lgn. [swissprot;acc:p81274]	Rooted			47.6504	36.9304	1.29028
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Ranked		0	12787.8	10454.7	1.22316
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Rooted	Subtracted		27.8028	22.9122	4.8906
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	Squared	Divided		492.157	225.924	2.17842
	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	Ranked	Subtracted		7584.72	9706.12	2121.4
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	Rooted	Divided		31.495	24.0263	1.31086
	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]	Measured	Divided	1	2353.63	3225.65	1.3705

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/