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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 168 to 217 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
168		gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	82.5916	98.0548	1.18722	
169	ATG3	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	82.5916	98.0548	1.18722	
170	TIA1	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	227.199	192.715	1.17894	
171	TIAL1	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	227.202	192.823	1.17829	
172	TIPRL	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [source:refseq;acc:nm_152902]	174.667	205.556	1.17685	
173	SNRPD1	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	227.032	193.056	1.17599	
174	DGCR14	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	335	286	1.17133	
175	COPS3	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	199.949	234.187	1.17123	
176	POLE4	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	275.754	235.908	1.1689	
177	NCBP2L	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	229.406	196.695	1.1663	
178		formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	226.887	194.72	1.1652	
179		huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	226.884	194.79	1.16476	
180	TARDBP	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	256.228	298.438	1.16474	
181	B9D1	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	229.818	267.265	1.16294	
182	HAT1	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	277.546	240.461	1.15422	
183	NCBP2	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	228.306	198.011	1.153	
184	OSR1	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	274.027	237.79	1.15239	
185	ADIPOR2	adiponectin receptor 2. [source:refseq;acc:nm_024551]	281.582	246.371	1.14292	
186	FLNB	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [source:refseq;acc:nm_001457]	226.582	198.444	1.14179	
187	REV1	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	226.582	198.444	1.14179	
188	PRMT1	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	226.582	198.444	1.14179	
189	PRMT8	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	226.582	198.444	1.14179	
190	SNRP70	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	226.582	198.444	1.14179	
191		filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	226.582	198.444	1.14179	
192	MSI2	musashi 2 isoform a. [source:refseq;acc:nm_138962]	227.491	199.458	1.14055	
193	MSI1	musashi 1. [source:refseq;acc:nm_002442]	227.491	199.458	1.14055	
194	ZC3H14	nuclear protein ukp68. [source:refseq;acc:nm_024824]	227.491	199.458	1.14055	
195	PRPF40B	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	227.971	200.417	1.13748	
196	FOXP4	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	263.215	231.407	1.13745	
197	FOXP1	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	263.215	231.407	1.13745	
198	FOXP3	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	263.191	231.394	1.13741	
199	EGFL8	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [source:swissprot;acc:q9umr5]	242.735	276.059	1.13729	
200	EGFL7	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	242.718	276.018	1.1372	
201	SF4	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	240.133	211.382	1.13601	
202	TRPC4	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	201.478	228.784	1.13553	
203	TBC1D10A	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	201.515	228.752	1.13516	
204	TRPC5	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	201.515	228.752	1.13516	
205	LUC7L2	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	228.1	200.968	1.13501	
206	LUC7L	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	228.085	201.006	1.13472	
207	PSEN2	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source:swissprot;acc:p49810]	285.684	252.234	1.13261	
208	SKP1A	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [source:swissprot;acc:p34991]	285.684	252.234	1.13261	
209	FBXW7	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [source:refseq;acc:nm_018315]	285.684	252.234	1.13261	
210	CUL2	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	285.684	252.234	1.13261	
211	PSEN1	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	285.684	252.234	1.13261	
212	CUL1	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	285.684	252.234	1.13261	
213	PLDN	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	210.693	186.95	1.127	
214	LASS2	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	191.644	170.192	1.12605	
215		myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	112	126	1.125	
216	MYH4	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	112	126	1.125	
217	MYH8	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	112	126	1.125	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/