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 383 to 432 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
383	RBM39	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	237.862	217.739	1.09242	
384	E2F1	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	266.421	244.236	1.09083	
385	E2F2	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	266.421	244.236	1.09083	
386	RPS14	40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	242.238	264.11	1.09029	
387		40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	242.238	264.11	1.09029	
388		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	227.575	208.756	1.09015	
389	SNRPF	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	227.575	208.756	1.09015	
390	MRPL13	60s ribosomal protein l13, mitochondrial (l13mt). [source:swissprot;acc:q9byd1]	241.828	263.62	1.09011	
391	RPS16	40s ribosomal protein s16. [source:swissprot;acc:p17008]	241.828	263.62	1.09011	
392	RPL13A	60s ribosomal protein l13a (23 kda highly basic protein). [source:swissprot;acc:p40429]	241.83	263.615	1.09008	
393	TXNL4A	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	225.719	207.072	1.09005	
394	DPP9	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [source:refseq;acc:nm_139159]	218.827	238.407	1.08948	
395	DPP8	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	218.827	238.407	1.08948	
396		putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	240.801	262.34	1.08945	
397	CCT3	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	110.689	101.613	1.08932	
398	ITGB1BP3	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	218.818	238.358	1.0893	
399	CLTC	clathrin heavy chain 1 (clh-17). [source:swissprot;acc:q00610]	207.889	226.226	1.08821	
400	PDCL	phosducin-like protein (phlp). [source:swissprot;acc:q13371]	207.908	226.218	1.08807	
401	RPA1	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [source:swissprot;acc:p27694]	207.908	226.218	1.08807	
402	RPA2	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [source:swissprot;acc:p15927]	207.908	226.218	1.08807	
403	PDC	phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	207.908	226.218	1.08807	
404	RAD52	dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	207.908	226.218	1.08807	
405	CLTCL1	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	207.931	226.209	1.0879	
406		transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	265.634	244.304	1.08731	
407	MRPS9	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [source:swissprot;acc:p82933]	239.75	260.544	1.08673	
408	CEBPZ	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [source:swissprot;acc:q03701]	255.112	234.804	1.08649	
409	POLR1E	rna polymerase i associated factor 53. [source:refseq;acc:nm_022490]	241.045	261.874	1.08641	
410		tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [source:swissprot;acc:q13888]	233.376	253.539	1.0864	
411	GTF2H1	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [source:swissprot;acc:p32780]	233.376	253.539	1.0864	
412	UQCRFSL1	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [source:swissprot;acc:p47985]	240.788	261.416	1.08567	
413	POLR1C	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [source:swissprot;acc:o15160]	240.913	261.45	1.08525	
414	KATNA1	katanin p60 subunit a 1. [source:refseq;acc:nm_007044]	232.431	252.238	1.08522	
415	KATNB1	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [source:refseq;acc:nm_005886]	232.382	252.166	1.08514	
416	POLR1B	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [source:swissprot;acc:q9h9y6]	240.6	261.041	1.08496	
417	SETMAR	set domain and mariner transposase fusion gene. [source:refseq;acc:nm_006515]	233.539	253.197	1.08417	
418	CLEC4M	cd209 antigen-like; putative type ii membrane protein. [source:refseq;acc:nm_014257]	233.539	253.197	1.08417	
419	FCER2	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [source:swissprot;acc:p06734]	233.539	253.197	1.08417	
420	CD209	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [source:refseq;acc:nm_021155]	233.539	253.197	1.08417	
421	TFIP11	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	223.202	205.9	1.08403	
422	RAB37	ras-related protein rab-37. [source:swissprot;acc:q96ax2]	240.287	260.193	1.08284	
423	RAB26	ras-related protein rab-26. [source:swissprot;acc:q9ulw5]	240.287	260.193	1.08284	
424	POLR2C	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [source:swissprot;acc:p19387]	240.287	260.193	1.08284	
425	MAX	max protein. [source:swissprot;acc:p25912]	227.828	210.561	1.082	
426	DCTN5	dynactin 4. [source:refseq;acc:nm_032486]	233.142	252.253	1.08197	
427	POLR2E	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [source:swissprot;acc:p19388]	239.977	259.525	1.08146	
428	DDX54	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	253.852	234.808	1.0811	
429	POLR3G	polymerase (rna) iii (dna directed) (32kd). [source:refseq;acc:nm_006467]	239.709	259.038	1.08064	
430	LSM5	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	227.748	210.888	1.07995	
431	TRUB1	trub pseudouridine (psi) synthase homolog 1. [source:refseq;acc:nm_139169]	236.245	255.113	1.07987	
432	ENDOG	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [source:swissprot;acc:q14249]	212.547	229.411	1.07934	

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/