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.

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1930 to 1979 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
242	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Rooted	0	23.9664	21.5733	1.11093
	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Squared	0	21584.2	16770.2	1.28706
	j domain containing protein 1. [swissprot;acc:q9ukb3]	Ranked	1	227.357	254.15	1.11785
	max protein. [swissprot;acc:p25912]	Measured		4640.26	5704.87	1.22943
	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]	Rooted		137.446	120.823	1.13758
	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]	Squared		42411.6	55802.1	1.31573
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Measured	0	729.216	642.343	1.13524
243	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	Rooted	0	28.4971	25.6518	1.11092
	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Measured	1	4246.95	5208.98	1.22652
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Measured	0	1225.09	1079.36	1.13502
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	Squared		8335.79	6506.81	1.28109
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Ranked		1251	1373	1.09752
	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	Ranked	1	227.357	254.15	1.11785
	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]	Squared		42411.6	55802.1	1.31573
	trophinin. [swissprot;acc:q12816]	Rooted		137.446	120.823	1.13758
244	60s ribosomal protein l23a. [swissprot;acc:p29316]	Rooted	0	22.6514	25.1571	1.11062
	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	Ranked	1	227.357	254.15	1.11785
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Squared	1	14728.8	19330.8	1.31245
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Measured	0	1225.09	1079.36	1.13502
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Ranked		10551.1	11579.9	1.09751
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	Squared		80.1214	102.556	1.28001
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Rooted	1	146.94	167.046	1.13683
	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	Measured		4250.14	5211.25	1.22614
245	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Squared		8875.01	6768.05	1.31131
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Rooted	0	22.6521	25.1534	1.11042
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Ranked	0	11867.6	13019	1.09702
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Measured	1	4251.65	5212.33	1.22595
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Measured	0	1225.09	1079.36	1.13502
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Rooted	1	146.94	167.046	1.13683
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	Squared	0	10596.4	8278.87	1.27993
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Ranked	1	226.109	202.333	1.11751
246	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Ranked		237.312	212.363	1.11748
	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Squared		8875.01	6768.05	1.31131
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	Squared	0	7273.2	9308.93	1.27989
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	Measured	1	4252.66	5213.05	1.22583
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Ranked	0	10551.6	11573.7	1.09687
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Measured		1225.09	1079.36	1.13502
	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	Rooted		12.8935	14.3151	1.11026
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Rooted	1	146.94	167.046	1.13683
247	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	Squared	0	20324.3	15893.2	1.2788
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Squared	1	8875.01	6768.05	1.31131
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Measured	0	1225.09	1079.36	1.13502
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Ranked		10551.6	11573.7	1.09687
	neurocalcin delta. [swissprot;acc:p29554]	Rooted		12.8769	11.6055	1.10955
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Rooted	1	47.3621	53.8355	1.13668
	rna-binding protein. [refseq;acc:nm_019027]	Ranked		237.302	212.41	1.11719
	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	Measured		6416.68	7865.15	1.22574
248	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	Ranked		237.302	212.41	1.11719
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Rooted	0	30.7397	27.7265	1.10868
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Ranked	0	10551.6	11573.7	1.09687

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/