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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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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 3708 to 3757 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
464	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Measured	1	4858.96	5568.85	1.1461
	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]	Squared	1	54726.7	45358.5	1.20654
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Measured	0	2290.09	2264.37	1.01136
	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]	Squared	0	18105.2	17795.2	1.01742
	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]	Rooted	1	50.2317	55.0025	1.09498
465	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Measured	0	6323	6254.09	1.01102
	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	Ranked	1	248.152	267.226	1.07686
	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	Squared	0	79185.5	77891.7	1.01661
	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]	Rooted	0	48.2804	48.8876	1.01258
	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]	Rooted	1	50.2317	55.0025	1.09498
	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	Measured	1	3847.31	4409.22	1.14605
	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	Ranked	0	9482.68	9620.66	1.01455
	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	Squared	1	25310.2	30537	1.20651
466	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	Ranked	1	248.152	267.226	1.07686
	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	Ranked	0	1543	1521	1.01446
		Rooted		78.4729	79.3914	1.0117
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Squared		363053	369010	1.01641
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	Measured		1467.74	1483.62	1.01082
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Squared	1	25513.6	30779.5	1.2064
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Measured		3847.31	4409.22	1.14605
	vav-3 protein. [swissprot;acc:q9ukw4]	Rooted		66.089	72.3555	1.09482
467	40s ribosomal protein s5. [swissprot;acc:p46782]	Rooted		50.4649	46.1093	1.09446
	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	Ranked		248.152	267.226	1.07686
	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Rooted	0	26.5153	26.8089	1.01107
	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	Ranked		21205	20914	1.01391
	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	Squared		13550.9	13764.5	1.01576
	metastasis-associated protein mta1. [swissprot;acc:q13330]	Measured	1	4864.25	5573.62	1.14583
	nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818]	Squared	1	23531.7	28371.6	1.20568
	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	Measured	0	2806.38	2782.56	1.00856
468	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	Measured	1	4869.15	5578.02	1.14558
	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	Squared	0	13550.9	13764.5	1.01576
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Squared	1	23531.7	28371.6	1.20568
	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	Rooted	0	38.9588	38.5391	1.01089
	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]	Ranked	0	21205	20914	1.01391
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Ranked	1	248.152	267.226	1.07686
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	Rooted	1	107.178	117.276	1.09422
	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	Measured	0	599.896	604.911	1.00836
469	60s ribosomal protein l9. [swissprot;acc:p32969]	Rooted	1	51.1334	46.7335	1.09415
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Ranked	1	248.152	267.226	1.07686
	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]	Ranked	0	21205	20914	1.01391
	importin 4. [refseq;acc:nm_024658]	Squared	0	379.863	374.561	1.01416
	nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303]	Squared	1	23531.7	28371.6	1.20568
	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	Measured	1	3831.17	4388.74	1.14554
	protein cgi-147. [swissprot;acc:q9y3e5]	Rooted	0	65.9667	66.6222	1.00994
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Measured		219.759	221.565	1.00822
470	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Squared		42.9529	43.56	1.01413
	block of proliferation 1. [swissprot;acc:q14137]	Measured	1	3796.24	4348.59	1.1455
	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]	Ranked	0	21205	20914	1.01391
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Measured	0	39165	39485	1.00817
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Ranked	1	248.152	267.226	1.07686

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/