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 193 to 242 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
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	
218	MYH2	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	112	126	1.125	
219	MYH3	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	112	126	1.125	
220	MYH1	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	112	126	1.125	
221		myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	112	126	1.125	
222	MYH7B	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	112	126	1.125	
223	MYH13	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	112	126	1.125	
224	SLC15A2	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	185.969	165.623	1.12285	
225	SNRPD2	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	226.471	201.769	1.12243	
226	COMP	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	239.991	269.238	1.12187	
227	THBS3	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	239.99	269.234	1.12186	
228	SH2D3C	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm_005489]	226.411	202.088	1.12036	
229	BCAR3	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	226.401	202.094	1.12028	
230	CSRP1	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	239.35	267.915	1.11934	
231	SHCBP1	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	239.336	267.881	1.11927	
232	CSRP2	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	239.336	267.879	1.11926	
233	CSRP3	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	239.32	267.842	1.11918	
234	CHRAC1	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	287.41	256.835	1.11905	
235	PAH	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	227.357	254.15	1.11785	
236	DUS1L	pp3111 protein. [source:refseq;acc:nm_022156]	227.357	254.15	1.11785	
237	STX18	syntaxin 18. [source:swissprot;acc:q9p2w9]	227.357	254.15	1.11785	
238		rd protein. [source:swissprot;acc:p18615]	227.357	254.15	1.11785	
239	GSTO1	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	227.357	254.15	1.11785	
240	AIG1	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	227.357	254.15	1.11785	
241	ATP5F1	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	227.357	254.15	1.11785	
242	DNAJC12	j domain containing protein 1. [source:swissprot;acc:q9ukb3]	227.357	254.15	1.11785	

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/