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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 780 to 829 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
390	MRPL13	60s ribosomal protein l13, mitochondrial (l13mt). [source:swissprot;acc:q9byd1]	Divided	241.828	263.62	1.09011	
391	RPS16	40s ribosomal protein s16. [source:swissprot;acc:p17008]	Divided	241.828	263.62	1.09011	
391	TXNL4A	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	Subtracted	225.719	207.072	18.647	
392	POLR3C	polymerase (rna) iii (dna directed) (62kd). [source:refseq;acc:nm_006468]	Subtracted	239.092	257.705	18.613	
392	RPL13A	60s ribosomal protein l13a (23 kda highly basic protein). [source:swissprot;acc:p40429]	Divided	241.83	263.615	1.09008	
393	POLR3F	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [source:swissprot;acc:q9h1d9]	Subtracted	238.921	257.327	18.406	
393	TXNL4A	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	Divided	225.719	207.072	1.09005	
394	CLTC	clathrin heavy chain 1 (clh-17). [source:swissprot;acc:q00610]	Subtracted	207.889	226.226	18.337	
394	DPP9	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [source:refseq;acc:nm_139159]	Divided	218.827	238.407	1.08948	
395	DPP8	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	Divided	218.827	238.407	1.08948	
395	PDCL	phosducin-like protein (phlp). [source:swissprot;acc:q13371]	Subtracted	207.908	226.218	18.31	
396		putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	Divided	240.801	262.34	1.08945	
396	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]	Subtracted	207.908	226.218	18.31	
397	CCT3	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	Divided	110.689	101.613	1.08932	
397	RPA2	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [source:swissprot;acc:p15927]	Subtracted	207.908	226.218	18.31	
398	ITGB1BP3	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	Divided	218.818	238.358	1.0893	
398	PDC	phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	Subtracted	207.908	226.218	18.31	
399	CLTC	clathrin heavy chain 1 (clh-17). [source:swissprot;acc:q00610]	Divided	207.889	226.226	1.08821	
399	RAD52	dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	Subtracted	207.908	226.218	18.31	
400	CLTCL1	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	Subtracted	207.931	226.209	18.278	
400	PDCL	phosducin-like protein (phlp). [source:swissprot;acc:q13371]	Divided	207.908	226.218	1.08807	
401	MKI67IP	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [source:refseq;acc:nm_032390]	Subtracted	254.434	236.224	18.21	
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]	Divided	207.908	226.218	1.08807	
402	NDC80	highly expressed in cancer, rich in leucine heptad repeats. [source:refseq;acc:nm_006101]	Subtracted	231.802	249.983	18.181	
402	RPA2	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [source:swissprot;acc:p15927]	Divided	207.908	226.218	1.08807	
403	MACF1	microtubule-actin crosslinking factor 1, isoform 4. [source:swissprot;acc:q96pk2]	Subtracted	228.468	246.338	17.87	
403	PDC	phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	Divided	207.908	226.218	1.08807	
404	DST	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [source:swissprot;acc:q03001]	Subtracted	228.463	246.33	17.867	
404	RAD52	dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	Divided	207.908	226.218	1.08807	
405	CLTCL1	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	Divided	207.931	226.209	1.0879	
405	GABARAP	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Subtracted	65.4586	83.0461	17.5875	
406		transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	Divided	265.634	244.304	1.08731	
406	NETO2	neuropilin- and tolloid-like protein 2 precursor. [source:refseq;acc:nm_018092]	Subtracted	237.109	254.667	17.558	
407	MRPS9	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [source:swissprot;acc:p82933]	Divided	239.75	260.544	1.08673	
407	NETO1	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [source:refseq;acc:nm_138966]	Subtracted	237.109	254.667	17.558	
408	CEBPZ	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [source:swissprot;acc:q03701]	Divided	255.112	234.804	1.08649	
408	HNRNPU	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [source:swissprot;acc:q00839]	Subtracted	237.109	254.667	17.558	
409	POLR1E	rna polymerase i associated factor 53. [source:refseq;acc:nm_022490]	Divided	241.045	261.874	1.08641	
409	RUNX2	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [source:swissprot;acc:q13950]	Subtracted	237.109	254.667	17.558	
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]	Divided	233.376	253.539	1.0864	
410	HNRPUL1	e1b-55kda-associated protein 5 isoform a. [source:refseq;acc:nm_007040]	Subtracted	237.109	254.667	17.558	
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]	Divided	233.376	253.539	1.0864	
411	RPL18	60s ribosomal protein l18. [source:swissprot;acc:q07020]	Subtracted	237.109	254.667	17.558	
412	NIP7	saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	Subtracted	251.926	234.547	17.379	
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]	Divided	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]	Divided	240.913	261.45	1.08525	
413	TFIP11	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Subtracted	223.202	205.9	17.302	
414	KATNA1	katanin p60 subunit a 1. [source:refseq;acc:nm_007044]	Divided	232.431	252.238	1.08522	
414	MAX	max protein. [source:swissprot;acc:p25912]	Subtracted	227.828	210.561	17.267	
415	KATNB1	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [source:refseq;acc:nm_005886]	Divided	232.382	252.166	1.08514	

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/