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.


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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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1308 to 1357 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
654	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	Subtracted	6455.66	7168.82	713.16	
655	dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	Divided	4088.63	4593.43	1.12346	
655	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	Subtracted	6441.14	7154.13	712.99	
656	apolipoprotein a-i binding protein; apoa-i binding protein. [source:refseq;acc:nm_144772]	Divided	6139.04	6893.7	1.12293	
656	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	Subtracted	6455.02	7167.96	712.94	
657	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [source:refseq;acc:nm_013366]	Subtracted	10341.2	9630.35	710.85	
657	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	Divided	6079.26	6824.47	1.12258	
658	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	Divided	6088.77	6834.87	1.12254	
658	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [source:swissprot;acc:o95817]	Subtracted	4522.71	5233.14	710.43	
659	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Subtracted	4858.96	5568.85	709.89	
659	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	Divided	6089.21	6835.34	1.12253	
660	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Subtracted	4864.25	5573.62	709.37	
660	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [source:swissprot;acc:q15695]	Divided	5575.18	6254.85	1.12191	
661	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [source:swissprot;acc:q09028]	Subtracted	4869.15	5578.02	708.87	
661	step ii splicing factor slu7. [source:refseq;acc:nm_006425]	Divided	5575.18	6254.85	1.12191	
662	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [source:swissprot;acc:o43639]	Subtracted	6776.85	7485.55	708.7	
662	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [source:swissprot;acc:q9byg4]	Divided	6374.65	7145.59	1.12094	
663	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [source:swissprot;acc:p48735]	Subtracted	7937.72	8646.38	708.66	
663	tubby protein homolog. [source:swissprot;acc:p50607]	Divided	6374.65	7145.59	1.12094	
664	pms1 protein homolog 2 (dna mismatch repair protein pms2). [source:swissprot;acc:p54278]	Subtracted	6231.31	6933.9	702.59	
664	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [source:swissprot;acc:p41743]	Divided	6374.65	7145.59	1.12094	
665	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	Subtracted	4108.15	4808.93	700.78	
665	numb protein homolog (h-numb) (protein s171). [source:swissprot;acc:p49757]	Divided	6374.65	7145.59	1.12094	
666	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [source:swissprot;acc:q15668]	Subtracted	6781.05	7480.15	699.1	
666	tbc1 domain family member 5. [source:swissprot;acc:q92609]	Divided	6374.65	7145.59	1.12094	
667	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	Subtracted	10075.5	9377.75	697.75	
667	tubby related protein 1 (tubby-like protein 1). [source:swissprot;acc:o00294]	Divided	6374.65	7145.59	1.12094	
668	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [source:swissprot;acc:q9y678]	Subtracted	10075.5	9377.75	697.75	
668	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [source:swissprot;acc:q9ubq0]	Divided	6374.65	7145.59	1.12094	
669	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [source:swissprot;acc:q9y3c3]	Subtracted	10075.5	9377.75	697.75	
669	numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	Divided	6374.65	7145.59	1.12094	
670	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [source:swissprot;acc:p48444]	Subtracted	10075.5	9377.75	697.75	
670	tubby related protein 3 (tubby-like protein 3). [source:swissprot;acc:o75386]	Divided	6374.65	7145.59	1.12094	
671	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [source:swissprot;acc:q9unp9]	Subtracted	10075.5	9377.75	697.75	
671	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [source:swissprot;acc:q96qk1]	Divided	6374.65	7145.59	1.12094	
672	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [source:swissprot;acc:q9p299]	Subtracted	10075.5	9377.75	697.75	
672	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	Divided	6374.65	7145.59	1.12094	
673	fibulin-1 precursor. [source:swissprot;acc:p23142]	Subtracted	8550.79	9248.06	697.27	
673	transcription factor btf3 (rna polymerase b transcription factor 3). [source:swissprot;acc:p20290]	Divided	6933.17	7766.54	1.1202	
674	hcv ns3-transactivated protein 1. [source:refseq;acc:nm_019048]	Subtracted	6000.23	6696.89	696.66	
674	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	Divided	5549.2	6215.42	1.12006	
675	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	Divided	5549.2	6215.42	1.12006	
675	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [source:swissprot;acc:p38606]	Subtracted	6000.23	6696.89	696.66	
676	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [source:swissprot;acc:p08243]	Subtracted	6000.23	6696.89	696.66	
676	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	Divided	5549.2	6215.42	1.12006	
677	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [source:swissprot;acc:q07864]	Subtracted	4024.4	4719.35	694.95	
677	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	Divided	5549.2	6215.42	1.12006	
678	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [source:swissprot;acc:p16333]	Subtracted	6784.67	7475.48	690.81	
678	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	Divided	6938.22	7770.65	1.11998	
679	adenylosuccinate synthase-like 1. [source:refseq;acc:nm_152328]	Divided	6503.1	7282.94	1.11992	

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/