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 3858 to 3907 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
483	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	Squared	0	312092	313482	1.00445
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Rooted	1	50.6084	55.2961	1.09263
	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]	Measured	1	9649.61	11053.5	1.14549
	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	Measured	0	20612.9	20672.6	1.0029
	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950]	Ranked	1	237.109	254.667	1.07405
	solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183]	Squared	1	26867.3	32335.2	1.20352
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Ranked	0	12223.8	12127.5	1.00794
484	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]	Ranked	1	237.109	254.667	1.07405
	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	Squared	0	311980	313369	1.00445
	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	Rooted	1	50.6084	55.2961	1.09263
	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]	Measured	1	9649.61	11053.5	1.14549
	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]	Ranked	0	11489.7	11414.3	1.00661
	scribble. [refseq;acc:nm_015356]	Measured	0	958.429	961.098	1.00278
	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4]	Squared	1	26867.2	32335	1.20351
	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	Rooted	0	24.2134	24.1232	1.00374
485	60s ribosomal protein l18. [swissprot;acc:q07020]	Ranked	1	237.109	254.667	1.07405
	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	Rooted	0	26.4223	26.5172	1.00359
	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	Measured		22850.1	22797.8	1.00229
	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	Squared		310884	312261	1.00443
	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	Ranked		12461.5	12542.3	1.00648
	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2]	Squared	1	26867.2	32335	1.20351
	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]	Measured		9649.61	11053.5	1.14549
	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]	Rooted		50.6084	55.2961	1.09263
486	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Rooted	0	20.6398	20.7123	1.00351
	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	Squared	0	310373	311745	1.00442
	histone h2b.e (h2b/e). [swissprot;acc:q99879]	Rooted	1	50.6084	55.2961	1.09263
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Ranked	0	13372.4	13288.3	1.00633
	mct-1 protein. [refseq;acc:nm_014060]	Ranked	1	226.313	243.03	1.07387
	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	Measured	0	22878.7	22826.8	1.00227
	secretory carrier-associated membrane protein 2. [swissprot;acc:o15127]	Squared	1	26865.9	32332.9	1.20349
	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	Measured	1	10908.6	12491.8	1.14513
487	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	Squared	0	68035.1	68294.1	1.00381
	mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]	Ranked	1	226.313	243.03	1.07387
	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	Rooted	0	12.5028	12.4629	1.0032
	pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328]	Measured	1	5277.4	6042.88	1.14505
	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]	Measured	0	250.419	249.857	1.00225
	secretory carrier-associated membrane protein 3. [swissprot;acc:o14828]	Squared	1	26865.9	32332.9	1.20349
	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	Ranked	0	13236.8	13159.3	1.00589
	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	Rooted	1	50.0015	54.627	1.09251
488	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	Measured	1	10872.4	12447	1.14483
	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655]	Squared	0	5487.61	5469.34	1.00334
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	Rooted	0	25.44	25.3889	1.00201
	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	Rooted	1	50.4315	46.1703	1.09229
	heat shock factor binding protein 1. [swissprot;acc:o75506]	Ranked	0	15204.2	15127.8	1.00505
	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]	Measured	0	250.419	249.857	1.00225
	secretory carrier-associated membrane protein 1. [swissprot;acc:o15126]	Squared	1	26866.1	32333.2	1.20349
	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146]	Ranked		225.026	209.798	1.07258
489	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	Rooted		50.5505	46.2797	1.09228
	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	Measured	0	22946.3	22895.1	1.00224
	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]	Rooted	0	22.997	22.9676	1.00128

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/