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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 Interaction Map Network Comparison Type Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2208 to 2257 of 14920 in total 
    Interaction Map	High confidence
    Network Comparison Type	Divided
    
Rank	description	Value Type	Filtered	red	green	network_comparison	
276	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [source:swissprot;acc:q96t37]	Measured	1	3119.98	2579.49	1.20953	
277	40s ribosomal protein s29. [source:swissprot;acc:p30054]	Ranked	1	241.849	267.642	1.10665	
277	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Ranked	0	11096.8	10251.6	1.08245	
277	adenylosuccinate synthase-like 1. [source:refseq;acc:nm_152328]	Rooted	0	24.1033	22.0791	1.09168	
277	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	Measured	0	870.93	975.647	1.12024	
277	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [source:swissprot;acc:p00491]	Squared	0	21885.1	17682.1	1.2377	
277	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [source:swissprot;acc:o76081]	Measured	1	3119.98	2579.49	1.20953	
277	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Rooted	1	65.9938	73.9449	1.12048	
277	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Squared	1	16120.1	20665.7	1.28198	
278	40s ribosomal protein s11. [source:swissprot;acc:p04643]	Ranked	1	241.399	267.088	1.10642	
278	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	Ranked	0	11644	10763.4	1.08181	
278	bystin. [source:swissprot;acc:q13895]	Squared	0	26569.7	32857.7	1.23666	
278	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [source:refseq;acc:nm_015247]	Rooted	0	34.0153	31.1803	1.09092	
278	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Squared	1	16120.1	20665.7	1.28198	
278	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Rooted	1	65.9938	73.9449	1.12048	
278	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [source:swissprot;acc:p51513]	Measured	0	2162.33	1932	1.11922	
278	transcription factor lbx1. [source:swissprot;acc:p52954]	Measured	1	3119.98	2579.49	1.20953	
279	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [source:swissprot;acc:q9nyg5]	Ranked	0	10614.2	9812.39	1.08171	
279	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [source:refseq;acc:nm_006614]	Measured	0	545.902	610.424	1.11819	
279	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	Rooted	0	33.1655	30.4161	1.09039	
279	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	Squared	0	229.508	283.721	1.23621	
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Ranked	1	252.644	228.42	1.10605	
279	mosaic protein lgn. [source:swissprot;acc:p81274]	Measured	1	3119.98	2579.49	1.20953	
279	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Squared	1	15569.5	19953.6	1.28158	
279	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Rooted	1	66.0989	74.0609	1.12046	
280	ba271b5.1 (similar to ribosomal protein s7). [source:sptrembl;acc:q9h1s9]	Squared	0	29812	36822.7	1.23516	
280	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Rooted	1	57.9068	64.8562	1.12001	
280	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132]	Rooted	0	28.8531	26.484	1.08945	
280	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	Ranked	0	10620.1	11471.2	1.08014	
280	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Ranked	1	252.512	228.356	1.10578	
280	musashi 1. [source:refseq;acc:nm_002442]	Squared	1	15569.5	19953.6	1.28158	
280	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [source:swissprot;acc:p32004]	Measured	0	545.902	610.424	1.11819	
280	regulator of g-protein signaling 17 (rgs17). [source:swissprot;acc:q9ugc6]	Measured	1	3119.98	2579.49	1.20953	
281	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Ranked	1	241.808	267.335	1.10557	
281	guanine nucleotide-binding protein g(o), alpha subunit 1. [source:swissprot;acc:p09471]	Measured	1	3119.98	2579.49	1.20953	
281	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Squared	1	15569.5	19953.6	1.28158	
281	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [source:swissprot;acc:q9nry6]	Ranked	0	12522.7	13514.5	1.0792	
281	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]	Squared	0	4275.32	3463.45	1.23441	
281	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	Rooted	0	27.1299	29.5494	1.08918	
281	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [source:swissprot;acc:q16594]	Measured	0	545.902	610.424	1.11819	
281	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	Rooted	1	57.9068	64.8562	1.12001	
282	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). [source:swissprot;acc:q09028]	Ranked	1	252.39	228.297	1.10553	
282	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [source:swissprot;acc:o43708]	Rooted	0	25.5082	23.4377	1.08834	
282	pepsin a precursor (ec 3.4.23.1). [source:swissprot;acc:p00790]	Measured	0	178.955	199.751	1.11621	
282	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	Squared	0	8755.38	7114.89	1.23057	
282	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	Measured	1	3119.98	2579.49	1.20953	
282	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source:swissprot;acc:q99961]	Ranked	0	8095.69	8732.68	1.07868	
282	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	Rooted	1	57.9819	64.9302	1.11984	
282	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	Squared	1	59704	76460.4	1.28066	
283	60s ribosomal protein l11. [source:swissprot;acc:p39026]	Ranked	1	241.828	267.346	1.10552	

Legend:
- Rank is the rank after comparing the two networks
- 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/