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 351 to 400 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
351	PEX1	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	242.14	265.696	1.09728	
352	TXNDC9	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	242.14	265.696	1.09728	
353	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	231.73	211.252	1.09694	
354	STX10	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	234.691	257.442	1.09694	
355	STX6	syntaxin 6. [source:swissprot;acc:o43752]	234.673	257.414	1.09691	
356		60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	243.24	266.796	1.09684	
357		60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	243.12	266.661	1.09683	
358	RPL10L	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	243.12	266.662	1.09683	
359	RPL4	60s ribosomal protein l4 (l1). [source:swissprot;acc:p36578]	239.277	262.434	1.09678	
360	SEC61G	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	243.072	266.559	1.09663	
361	MRPL17	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	242.83	266.248	1.09644	
362	SHROOM2	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	231.492	211.136	1.09641	
363	SHROOM3	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	231.481	211.131	1.09639	
364	POLR2B	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	243.208	266.617	1.09625	
365	MRPL36	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	242.744	266.07	1.09609	
366	RPS5	40s ribosomal protein s5. [source:swissprot;acc:p46782]	242.473	265.756	1.09602	
367	HNRPM	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [source:swissprot;acc:p52272]	234.146	256.627	1.09601	
368	PUS1	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [source:swissprot;acc:q9y606]	242.66	265.715	1.09501	
369	MRPL12	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	242.159	265.104	1.09475	
370	NUDT12	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	242.159	265.104	1.09475	
371	RPS6KC1	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	186.52	170.42	1.09447	
372		ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	186.52	170.42	1.09447	
373	MRPL11	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	242.37	265.255	1.09442	
374	TFDP2	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	267.208	244.168	1.09436	
375	POLR3A	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	242.686	265.516	1.09407	
376	DDX56	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	257.017	234.945	1.09395	
377	POLR1A	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	242.691	265.481	1.09391	
378	RPL30	60s ribosomal protein l30. [source:swissprot;acc:p04645]	242.593	265.365	1.09387	
379	AK2	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	241.509	264.163	1.0938	
380		suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	242.109	264.79	1.09368	
381	TAF7	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	200.586	183.423	1.09357	
382	TAF7L	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [source:refseq;acc:nm_024885]	200.791	183.66	1.09328	
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	

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/