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 1351 to 1400 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
169	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Measured	1	23693.7	18263	1.29736
169	symplekin. [swissprot;acc:q92797]	Squared		124118	88668.8	1.39979
170	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	Rooted		53.4993	45.9227	1.16499
	calcyphosine. [swissprot;acc:q13938]	Squared	0	175.528	276.854	1.57726
	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	Squared	1	96730.5	69286.7	1.39609
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Ranked	0	11364	12941	1.13877
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Measured	1	23693.7	18263	1.29736
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Ranked	1	227.199	192.715	1.17894
	serpin b11. [swissprot;acc:q96p15]	Rooted	0	6.48074	7.48331	1.1547
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Measured	0	112.666	141.702	1.25772
171	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	Squared	1	96602.7	69211.2	1.39577
	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	Rooted	0	6.48074	7.48331	1.1547
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Rooted	1	61.6639	71.7355	1.16333
	lamin b2. [swissprot;acc:q03252]	Ranked	0	12135.4	13802	1.13733
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Measured	1	23693.7	18263	1.29736
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Ranked	1	227.202	192.823	1.17829
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Squared	0	1592.06	2488.07	1.5628
	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	Measured	0	112.666	141.702	1.25772
172	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Ranked	1	174.667	205.556	1.17685
	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	Squared	1	121579	87259.3	1.39331
	likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]	Squared	0	47.4746	74.0536	1.55986
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Rooted	0	40.4536	35.073	1.15341
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Rooted	1	56.7592	65.9889	1.16261
	trophinin. [swissprot;acc:q12816]	Measured	1	23693.7	18263	1.29736
	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	Measured	0	112.666	141.702	1.25772
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Ranked	0	12225.7	13893.1	1.13638
173	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Rooted	1	145.551	168.796	1.1597
	60s ribosomal protein l7. [swissprot;acc:p18124]	Rooted	0	27.512	31.7228	1.15305
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Measured	1	4579.34	5940.64	1.29727
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Measured	0	3265.25	4102.97	1.25656
	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]	Squared	0	48.239	75.2348	1.55963
	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]	Squared	1	82624.3	115061	1.39258
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Ranked	1	227.032	193.056	1.17599
	suppressor of actin 1. [refseq;acc:nm_014016]	Ranked	0	19088.1	16804.6	1.13589
174	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Rooted		15.8745	18.303	1.15298
	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]	Squared		48.3438	75.3968	1.5596
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Ranked	1	335	286	1.17133
	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Measured	0	488.43	612.604	1.25423
	mad protein (max dimerizer). [swissprot;acc:q05195]	Measured	1	4455.95	5774.03	1.2958
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Rooted	1	145.551	168.796	1.1597
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	Ranked	0	13248.5	11666.4	1.13561
	sedlin. [swissprot;acc:o14582]	Squared	1	112820	157033	1.39189
175	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	Ranked	1	199.949	234.187	1.17123
	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	Measured	0	1382.5	1107	1.24887
	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	Squared	0	48.5538	75.7214	1.55954
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Measured	1	4456.67	5773.77	1.29553
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Rooted	0	61.6393	70.9983	1.15183
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Rooted	1	145.551	168.796	1.1597
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Squared	1	112820	157033	1.39189
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	Ranked	0	13248.5	11666.4	1.13561

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/