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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Gene Rank description Value Type Filtered Network Comparison Type Interaction Map red network_comparison green

Results: HTML CSV LaTeX

Showing element 2632 to 2681 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	network_comparison	green
329	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	Rooted	0	15.4404	1.05642	16.3116
330	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Measured	0	1658.23	1.08882	1805.52
	60s ribosomal protein l32. [swissprot;acc:p02433]	Rooted	1	50.519	1.1091	45.5497
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Ranked	1	312	1.09859	284
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Rooted	0	57.5016	1.05608	60.7262
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Squared	0	2758.07	1.14635	3161.7
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Squared	1	16203.4	1.25529	20339.9
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Ranked	0	12320.2	1.05668	13018.5
	septin 6. [swissprot;acc:q14141]	Measured	1	15959.9	1.1878	18957.1
331	40s ribosomal protein s3a. [swissprot;acc:p49241]	Ranked	0	10405.1	1.05644	10992.4
	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Squared		26.2121	1.14497	22.8932
	alpha-nac protein. [sptrembl;acc:q9h009]	Rooted		9.95878	1.05459	9.44328
	apical-like protein (apxl protein). [swissprot;acc:q13796]	Rooted	1	60.6697	1.10896	67.2802
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Ranked	1	312	1.09859	284
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Measured	0	4088	1.0888	4451
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Measured	1	20287.2	1.18751	17083.8
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Squared	1	33100.3	1.25439	41520.6
332	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Measured	0	15411.3	1.08783	14167
	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Rooted		15.297	1.05434	14.5086
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Squared		3693.52	1.14263	3232.47
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Ranked		8125.5	1.0556	7697.5
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Ranked	1	312	1.09859	284
	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	Squared		14464.3	1.25432	18142.8
	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Measured		5051.16	1.183	5975.51
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Rooted		60.6732	1.10894	67.2827
333	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Rooted	0	105.939	1.05422	111.683
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Squared		3680.39	1.14207	3222.57
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Ranked		8125.5	1.0556	7697.5
	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Ranked	1	312	1.09859	284
	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Measured		5039.63	1.18299	5961.83
	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	Rooted		49.0526	1.10857	54.3781
	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Squared		14464.3	1.25432	18142.8
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Measured	0	634.305	1.0857	584.237
334	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	Squared	1	64975.9	1.24894	81151.2
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Rooted	0	10.603	1.05418	10.0581
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Squared		3680.47	1.14207	3222.63
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Ranked		8125.5	1.0556	7697.5
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Ranked	1	312	1.09859	284
	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	Measured	0	3161.12	1.0808	2924.8
	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Rooted	1	58.6096	1.10844	64.9655
	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]	Measured		14924.4	1.18298	17655.2
335	40s ribosomal protein s11. [swissprot;acc:p04643]	Rooted		50.4705	1.10841	45.5342
	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	Rooted	0	24.2756	1.05406	25.588
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Ranked	1	312	1.09859	284
	germ cell-less. [refseq;acc:nm_022471]	Measured	0	1829.81	1.08014	1694.05
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Squared		3680.43	1.14207	3222.6
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Ranked		8125.5	1.0556	7697.5
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Measured	1	3494.31	1.18181	4129.6
	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	Squared		30651.3	1.24802	38253.3
336	60s ribosomal protein l11. [swissprot;acc:p39026]	Rooted		50.3167	1.10814	45.4063

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/