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 description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 782 to 831 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	green	red	network_comparison	
391	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	0	14738.5	14223.9	1.03618	
392	60s ribosomal protein l13a (23 kda highly basic protein). [source:swissprot;acc:p40429]	1	263.615	241.83	1.09008	
392	seven in absentia homolog 1. [source:refseq;acc:nm_003031]	0	10201.4	9854.67	1.03518	
393	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	1	207.072	225.719	1.09005	
393	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [source:swissprot;acc:p23193]	0	13010	12576	1.03451	
394	60s ribosomal protein l12. [source:swissprot;acc:p30050]	0	9857.79	10196.9	1.0344	
394	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [source:refseq;acc:nm_139159]	1	238.407	218.827	1.08948	
395	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	1	238.407	218.827	1.08948	
395	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	0	9856.7	10195.5	1.03437	
396	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	0	9856.12	10194.8	1.03436	
396	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	1	262.34	240.801	1.08945	
397	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	0	9676.53	10006.9	1.03414	
397	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	1	101.613	110.689	1.08932	
398	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:p32189]	0	17267.9	16699.2	1.03406	
398	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	1	238.358	218.818	1.0893	
399	clathrin heavy chain 1 (clh-17). [source:swissprot;acc:q00610]	1	226.226	207.889	1.08821	
399	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14409]	0	17271.4	16703.1	1.03402	
400	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14410]	0	17278.4	16711	1.03395	
400	phosducin-like protein (phlp). [source:swissprot;acc:q13371]	1	226.218	207.908	1.08807	
401	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]	1	226.218	207.908	1.08807	
401	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	0	11904.9	12305.9	1.03368	
402	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [source:swissprot;acc:q9y6q5]	0	10918	10562.4	1.03367	
402	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [source:swissprot;acc:p15927]	1	226.218	207.908	1.08807	
403	phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	1	226.218	207.908	1.08807	
403	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [source:swissprot;acc:o75795]	0	10111.2	9783.63	1.03348	
404	dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	1	226.218	207.908	1.08807	
404	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [source:swissprot;acc:o75310]	0	10111.2	9783.63	1.03348	
405	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	1	226.209	207.931	1.0879	
405	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [source:swissprot;acc:p06133]	0	10111.2	9783.63	1.03348	
406	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [source:swissprot;acc:q07075]	0	10111.2	9783.63	1.03348	
406	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	1	244.304	265.634	1.08731	
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [source:swissprot;acc:p82933]	1	260.544	239.75	1.08673	
407	udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [source:swissprot;acc:p36537]	0	10111.2	9783.63	1.03348	
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [source:swissprot;acc:q03701]	1	234.804	255.112	1.08649	
408	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [source:swissprot;acc:p54855]	0	10111.2	9783.63	1.03348	
409	rna polymerase i associated factor 53. [source:refseq;acc:nm_022490]	1	261.874	241.045	1.08641	
409	similar to cg7020 gene product (fragment). [source:sptrembl;acc:q96ib4]	0	10945.3	10598.5	1.03272	
410	histone h4. [source:swissprot;acc:p02304]	0	9308.99	9611.37	1.03248	
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]	1	253.539	233.376	1.0864	
411	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [source:swissprot;acc:p35268]	0	12508.3	12115.7	1.0324	
411	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]	1	253.539	233.376	1.0864	
412	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	0	8279.69	8546.06	1.03217	
412	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [source:swissprot;acc:p47985]	1	261.416	240.788	1.08567	
413	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [source:swissprot;acc:o15160]	1	261.45	240.913	1.08525	
413	protein cgi-147. [source:swissprot;acc:q9y3e5]	0	5298.12	5135.25	1.03172	
414	germ cell-less. [source:refseq;acc:nm_022471]	0	10644.4	10978.8	1.03142	
414	katanin p60 subunit a 1. [source:refseq;acc:nm_007044]	1	252.238	232.431	1.08522	
415	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [source:refseq;acc:nm_005886]	1	252.166	232.382	1.08514	
415	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [source:swissprot;acc:o15525]	0	13166.3	13571.2	1.03075	
416	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [source:swissprot;acc:q9h9y6]	1	261.041	240.6	1.08496	

Legend:
- Rank is the rank after comparing the two networks
- 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/