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 Filtered green Interaction Map red network_comparison

Results: HTML CSV LaTeX

Showing element 301 to 350 of 9634 in total

Value Type

: Measured
Network Comparison Type

: Divided

Rank	description	Filtered	green	Interaction Map	red	network_comparison
76	cab2. [refseq;acc:nm_033419]	0	128.776	Low confidence	72.5877	1.77407
	dead-box protein. [refseq;acc:nm_018665]	0	183	High confidence	313.667	1.71403
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	5933.4	Low confidence	5334.13	1.11235
	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]	1	3058.57	High confidence	4599.26	1.50373
77	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	0	2804	Low confidence	1593	1.7602
	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	0	416.524	High confidence	712.071	1.70956
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1	5933.4	Low confidence	5334.13	1.11235
	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]		3093.6	High confidence	4612.39	1.49095
78	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		7132.71		4800.81	1.48573
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	0	95		161	1.69474
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	1	5933.4	Low confidence	5334.13	1.11235
	protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479]	0	112.5		189	1.68
79	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	1	5933.4		5334.13	1.11235
	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	0	572.008		341.484	1.67507
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	0	544.991	High confidence	323.79	1.68316
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	1	4567.51		3074.57	1.48558
80	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	1	5945.32		4133.47	1.43834
	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	0	493		293	1.68259
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	1	5933.4	Low confidence	5334.13	1.11235
	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	0	50	Low confidence	30	1.66667
81	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	1	5943.56	High confidence	4136.36	1.43691
	regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924]	1	6146.97	Low confidence	5528.68	1.11183
	tolloid-like 1. [refseq;acc:nm_012464]	0	688.237	Low confidence	413.072	1.66614
	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]		50	High confidence	30	1.66667
82	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]		115.333	High confidence	191.333	1.65896
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	1	7884.98	Low confidence	7098.44	1.1108
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	1	5954.48	High confidence	4172.91	1.42694
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	0	499.295	Low confidence	300.638	1.66078
83	abl-philin 2. [refseq;acc:nm_032327]		29	Low confidence	48	1.65517
	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]		100.887	High confidence	166.114	1.64654
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	1	7033.29	High confidence	4932.27	1.42597
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]		7794.8	Low confidence	7030.67	1.10869
84	jun dimerization protein. [refseq;acc:nm_130469]		7033.29	High confidence	4932.27	1.42597
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	0	1601.52	High confidence	973.698	1.64478
	sedlin. [swissprot;acc:o14582]	0	299.876	Low confidence	181.896	1.64861
	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	1	12351.1	Low confidence	11141.5	1.10857
85	fos-related antigen 2. [swissprot;acc:p15408]	1	7037.11	High confidence	4941.95	1.42395
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	0	1361.92	Low confidence	840.74	1.61991
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	0	1106.88	High confidence	679.449	1.62908
	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	1	7797.14	Low confidence	7034.43	1.10843
86	alpha crystallin a chain. [swissprot;acc:p02489]	0	89.2447	High confidence	55.3059	1.61366
	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	0	201.455	Low confidence	325.337	1.61494
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	1	7037.32	High confidence	4942.49	1.42384
	vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269]	1	8046.29	Low confidence	7263.76	1.10773
87	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	0	81.6539	Low confidence	129.715	1.5886
	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	1	7038.04	High confidence	4944.3	1.42347
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	0	483.809	High confidence	304.664	1.58801
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	1	7809.38	Low confidence	7054.1	1.10707
88	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	0	54.6667	Low confidence	34.6667	1.57692
88	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	1	1695.45	High confidence	2411.93	1.42259

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/