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 373 to 422 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
47	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Squared	0	975.125	178.265	5.47009
	gbp protein isoform a. [refseq;acc:nm_017870]	Ranked	1	325.586	256.492	1.26938
	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	Measured	0	202.156	438.016	2.16672
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Squared	1	98517.9	56927.2	1.73059
48	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Measured	0	870.482	403.196	2.15895
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Measured	1	779.167	1390.33	1.78438
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Ranked	1	65.4586	83.0461	1.26868
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Squared	0	960.518	176.164	5.45241
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Squared	1	6300.2	10703.5	1.69891
	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	Ranked	0	9830	6909	1.42278
	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Rooted	1	27.7254	44.0299	1.58807
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Rooted	0	15.0533	9.31487	1.61605
49	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Squared	1	28994.2	17134.8	1.69212
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Ranked	1	133	105	1.26667
	brain protein 16. [refseq;acc:nm_016458]	Ranked	0	6890.54	4854.99	1.41927
	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	Squared	0	8.10857	43.7473	5.39519
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Rooted	1	27.7254	44.0299	1.58807
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Measured	1	779.167	1390.33	1.78438
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	Rooted	0	14.1508	8.89106	1.59158
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Measured	0	72	151	2.09722
50	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Ranked	1	133	105	1.26667
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Ranked	0	9249.73	13091.4	1.41533
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Rooted	0	11.0328	6.96286	1.58452
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Rooted	1	27.7254	44.0299	1.58807
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Measured	1	779.167	1390.33	1.78438
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	Squared	0	10.974	2.38124	4.60852
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Squared	1	28994.2	17134.8	1.69212
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Measured	0	44	21	2.09524
51	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	Squared	0	0.872309	3.99932	4.58475
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Squared	1	28994.2	17134.8	1.69212
	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	Ranked	0	7168	5102	1.40494
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Rooted	1	27.7254	44.0299	1.58807
	nanos (fragment). [sptrembl;acc:q8wy41]	Rooted	0	19.4165	12.2882	1.58009
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Measured	1	779.167	1390.33	1.78438
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	Measured	0	184.422	88.5622	2.0824
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Ranked	1	133	105	1.26667
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		1	133	105	1.26667
	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]		0	3284	4554.5	1.38688
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Measured	1	779.167	1390.33	1.78438
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Measured	0	999.28	481.725	2.07438
	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	Rooted	0	16.3095	25.3969	1.55718
	neuralized-like. [refseq;acc:nm_004210]	Rooted	1	27.9107	44.1656	1.58239
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Squared	1	28994.2	17134.8	1.69212
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Squared	0	1.22698	5.39669	4.39835
53	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Rooted	0	11.844	18.0183	1.5213
	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]	Measured	1	779.167	1390.33	1.78438
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Measured	0	420.365	861.814	2.05016
	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	1	30.8986	46.4619	1.50369
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Squared	1	28994.2	17134.8	1.69212
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Squared	0	0.458225	0.104379	4.39001

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/