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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2018 to 2067 of 3228 in total 
    Value Type	Measured
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	red	green	network_comparison	
2018	mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [source:swissprot;acc:p30039]	6555.42	6938.82	1.05849	
2019	lysophospholipase ii; acyl-protein thioesterase. [source:refseq;acc:nm_007260]	6555.42	6938.82	1.05849	
2020	diphthamide biosynthesis-like protein 2. [source:refseq;acc:nm_001384]	4935.84	5224.27	1.05844	
2021	kinesin-like protein kif3c. [source:swissprot;acc:o14782]	5934.68	6281.49	1.05844	
2022	enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [source:refseq;acc:nm_014666]	5520.26	5841.16	1.05813	
2023	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	3560.24	3364.84	1.05807	
2024	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [source:swissprot;acc:o15392]	5976.81	6323.87	1.05807	
2025	candidate tumor suppressor in ovarian cancer 2. [source:refseq;acc:nm_080822]	4813.13	5091.36	1.05781	
2026	aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [source:swissprot;acc:p14868]	6766.45	7155.54	1.0575	
2027	rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [source:refseq;acc:nm_004584]	6218.34	6575.81	1.05749	
2028	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [source:swissprot;acc:q15233]	10243.4	9686.82	1.05746	
2029	paraspeckle protein 1. [source:refseq;acc:nm_018282]	10241.3	9685.21	1.05742	
2030	histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [source:swissprot;acc:q9h5i1]	5060.82	5350.93	1.05732	
2031	eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [source:swissprot;acc:p05198]	5060.82	5350.93	1.05732	
2032	histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [source:swissprot;acc:o43463]	5060.82	5350.93	1.05732	
2033	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	6101.12	6449.87	1.05716	
2034	topoisomerase (dna) ii binding protein. [source:refseq;acc:nm_007027]	6920.71	7315.59	1.05706	
2035	acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [source:swissprot;acc:q15067]	6920.71	7315.59	1.05706	
2036	atp synthase f chain, mitochondrial (ec 3.6.3.14). [source:swissprot;acc:p56134]	6920.71	7315.59	1.05706	
2037	probable atp-dependent helicase ddx35 (deah-box protein 35). [source:swissprot;acc:q9h5z1]	6920.71	7315.59	1.05706	
2038	transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [source:swissprot;acc:p49848]	7088.08	7492.23	1.05702	
2039	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	3646.01	3449.54	1.05696	
2040	rho-gtpase-activating protein 8. [source:swissprot;acc:q9nsg0]	6036.68	6379.44	1.05678	
2041	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]	6036.68	6379.44	1.05678	
2042	kinesin light chain 2 (klc 2). [source:swissprot;acc:q9h0b6]	6036.62	6379.38	1.05678	
2043	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [source:swissprot;acc:p33176]	6036.68	6379.44	1.05678	
2044	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [source:swissprot;acc:o60282]	6036.68	6379.44	1.05678	
2045	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [source:swissprot;acc:q12840]	6036.68	6379.44	1.05678	
2046	kinesin light chain 1 (klc 1). [source:swissprot;acc:q07866]	6036.73	6379.48	1.05678	
2047	transcription factor iiia (factor a) (tfiiia). [source:swissprot;acc:q92664]	6036.68	6379.44	1.05678	
2048	exocyst complex component sec3 (bm-012). [source:swissprot;acc:q9nv70]	6036.68	6379.44	1.05678	
2049	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [source:refseq;acc:nm_003075]	5634.94	5953.19	1.05648	
2050	adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [source:swissprot;acc:p21851]	5556.36	5870.11	1.05647	
2051	60s ribosomal protein l26. [source:swissprot;acc:q02877]	3601.97	3409.48	1.05646	
2052	polybromo 1. [source:refseq;acc:nm_018165]	5634.8	5952.7	1.05642	
2053	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [source:refseq;acc:nm_003601]	5634.8	5952.7	1.05642	
2054	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [source:swissprot;acc:p51532]	5634.8	5952.7	1.05642	
2055	possible global transcription activator snf2l1. [source:swissprot;acc:p28370]	5634.8	5952.7	1.05642	
2056	tbp-associated factor 172 (taf-172) (taf(ii)170). [source:swissprot;acc:o14981]	5634.8	5952.7	1.05642	
2057	possible global transcription activator snf2l2 (snf2-alpha). [source:swissprot;acc:p51531]	5634.8	5952.7	1.05642	
2058	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [source:swissprot;acc:p56377]	5552.69	5865.84	1.0564	
2059	adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [source:swissprot;acc:o43747]	5552.69	5865.84	1.0564	
2060	adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [source:swissprot;acc:q96pc3]	5552.69	5865.84	1.0564	
2061	adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [source:swissprot;acc:q00382]	5552.69	5865.84	1.0564	
2062	adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [source:swissprot;acc:o75843]	5552.7	5865.85	1.0564	
2063	swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [source:refseq;acc:nm_003074]	5634.63	5952.14	1.05635	
2064	adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [source:swissprot;acc:q10567]	5548.79	5861.31	1.05632	
2065	60s ribosomal protein l35. [source:swissprot;acc:p42766]	3602.25	3410.23	1.05631	
2066	similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [source:sptrembl;acc:q96ek6]	5882.61	6213.34	1.05622	
2067	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	3602.75	3411.18	1.05616	

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/