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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 2480 to 2529 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
2480	ARHGAP1	rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [source:swissprot;acc:q07960]	218.093	218.72	1.00287	
2481	KLC2	kinesin light chain 2 (klc 2). [source:swissprot;acc:q9h0b6]	218.093	218.72	1.00287	
2482	KIF5B	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [source:swissprot;acc:p33176]	218.093	218.72	1.00287	
2483	KIF5C	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [source:swissprot;acc:o60282]	218.093	218.72	1.00287	
2484	KIF5A	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [source:swissprot;acc:q12840]	218.093	218.72	1.00287	
2485	KLC1	kinesin light chain 1 (klc 1). [source:swissprot;acc:q07866]	218.093	218.72	1.00287	
2486	GTF3A	transcription factor iiia (factor a) (tfiiia). [source:swissprot;acc:q92664]	218.093	218.72	1.00287	
2487	EXOC1	exocyst complex component sec3 (bm-012). [source:swissprot;acc:q9nv70]	218.093	218.72	1.00287	
2488		hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [source:refseq;acc:nm_023934]	194.527	195.08	1.00284	
2489		dc11 protein. [source:refseq;acc:nm_020186]	194.527	195.08	1.00284	
2490	APPBP1	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [source:refseq;acc:nm_003905]	194.527	195.08	1.00284	
2491	ALAS2	5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [source:swissprot;acc:p22557]	194.527	195.08	1.00284	
2492	UBE1C	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [source:refseq;acc:nm_003968]	194.527	195.08	1.00284	
2493	UBE1	ubiquitin-activating enzyme e1 (a1s9 protein). [source:swissprot;acc:p22314]	194.527	195.08	1.00284	
2494	SLC25A12	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [source:swissprot;acc:o75746]	194.527	195.08	1.00284	
2495	HHAT	melanoma antigen recognized by t cells 2. [source:refseq;acc:nm_018194]	194.527	195.08	1.00284	
2496	ALAS1	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	194.527	195.08	1.00284	
2497	SLC25A13	calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [source:swissprot;acc:q9ujs0]	194.527	195.08	1.00284	
2498	NDUFAB1	acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [source:swissprot;acc:o14561]	194.527	195.08	1.00284	
2499	NOB1	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [source:refseq;acc:nm_014062]	231.414	230.76	1.00283	
2500	BIRC5	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [source:swissprot;acc:o15392]	218.949	219.552	1.00275	
2501	ZMYND8	protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [source:swissprot;acc:q9ulu4]	217.398	216.809	1.00272	
2502	ZMYND11	adenovirus 5 e1a-binding protein (bs69 protein). [source:swissprot;acc:q15326]	217.417	216.844	1.00264	
2503	PSMC1	26s protease regulatory subunit 4 (p26s4). [source:swissprot;acc:q03527]	215.581	216.137	1.00258	
2504	TNS1	tensin. [source:refseq;acc:nm_022648]	218.238	217.682	1.00255	
2505	CBX5	chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [source:swissprot;acc:p45973]	187.853	188.326	1.00252	
2506	C10orf83	44050 protein. [source:refseq;acc:nm_178832]	151.386	151.009	1.0025	
2507	PPP1R8	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [source:swissprot;acc:q12972]	151.386	151.009	1.0025	
2508	CEECAM1	cerebral cell adhesion molecule. [source:refseq;acc:nm_016174]	194.349	193.871	1.00247	
2509	CBX3	chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [source:swissprot;acc:q13185]	187.902	188.366	1.00247	
2510	GRPEL2	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [source:swissprot;acc:q8taa5]	234.384	234.948	1.00241	
2511	GRPEL1	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [source:swissprot;acc:q9hav7]	234.384	234.948	1.00241	
2512	SMARCD2	swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [source:refseq;acc:nm_003077]	234.384	234.948	1.00241	
2513	SMARCD3	swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [source:refseq;acc:nm_003078]	234.384	234.948	1.00241	
2514	SMARCD1	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [source:swissprot;acc:q96gm5]	234.384	234.948	1.00241	
2515	DFFB	dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [source:swissprot;acc:o76075]	215.835	216.341	1.00234	
2516	ADAMTS9	adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [source:swissprot;acc:q9p2n4]	215.835	216.341	1.00234	
2517	DFFA	dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [source:swissprot;acc:o00273]	215.835	216.341	1.00234	
2518	ANK3	ankyrin 3 (ank-3) (ankyrin g). [source:swissprot;acc:q12955]	215.835	216.341	1.00234	
2519	ANK2	ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [source:swissprot;acc:q01484]	215.835	216.341	1.00234	
2520	ARL3	adp-ribosylation factor-like protein 3. [source:swissprot;acc:p36405]	215.835	216.341	1.00234	
2521		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	201.96	201.488	1.00234	
2522	UNC119	unc-119 protein homolog (retinal protein 4) (hrg4). [source:swissprot;acc:q13432]	215.835	216.341	1.00234	
2523	KPNB1	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [source:swissprot;acc:q14974]	201.96	201.488	1.00234	
2524	TBL1X	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [source:swissprot;acc:o60907]	201.96	201.488	1.00234	
2525	PSMD8	26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [source:swissprot;acc:p48556]	215.835	216.341	1.00234	
2526	TBL1Y	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	201.96	201.488	1.00234	
2527	TKTL1	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [source:swissprot;acc:p51854]	209.143	208.659	1.00232	
2528	SCRIB	scribble. [source:refseq;acc:nm_015356]	221.782	222.291	1.0023	
2529	LRRC1	lap (leucine-rich repeats and pdz) and no pdz protein. [source:refseq;acc:nm_018214]	221.776	222.283	1.00229	

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/