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 red green network_comparison
Results: HTML CSV LaTeX Showing element 7864 to 7913 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1966 rd protein. [swissprot;acc:p18615] Measured 4374.32 4126.96 1.05994
1967 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 3678.56 3470.55
choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] Ranked 211.632 213.702 1.00978
cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] Squared 24782.4 27081.1 1.09276
histidine-rich membrane protein ke4. [swissprot;acc:q92504] Rooted 63.8906 65.6826 1.02805
1968 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Squared 24782.4 27081.1 1.09276
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Measured 4374.32 4126.96 1.05994
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] Rooted 63.8906 65.6826 1.02805
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Ranked 211.633 213.703 1.00978
1969 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Measured 4374.32 4126.96 1.05994
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Squared 24782.4 27081.1 1.09276
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Rooted 63.8903 65.6821 1.02804
1970 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Measured 4374.32 4126.96 1.05994
importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] Ranked 211.62 213.683 1.00975
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Squared 24782.4 27081.1 1.09276
microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] Rooted 63.8904 65.6822 1.02804
1971 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] 59.346 61.0071 1.02799
creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Ranked 198.258 196.346 1.00974
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Squared 24782.4 27081.1 1.09276
j domain containing protein 1. [swissprot;acc:q9ukb3] Measured 4374.32 4126.96 1.05994
1972 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Squared 24782.4 27081.1 1.09276
regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] Ranked 219.777 217.659 1.00973
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Rooted 63.8804 65.6665 1.02796
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Measured 4374.32 4126.96 1.05994
1973 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Squared 24782.4 27081.1 1.09276
glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] Rooted 62.5647 64.3135 1.02795
wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] Ranked 214.611 212.546 1.00972
1974 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Measured 3678.62 3470.64 1.05993
dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Squared 24782.4 27081.1 1.09276
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Rooted 63.6643 65.4435 1.02795
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Ranked 214.611 212.546 1.00972
1975 cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] Measured 6988.29 7406.53 1.05985
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Rooted 63.6643 65.4435 1.02795
sestrin 3. [swissprot;acc:p58005] Squared 24782.4 27081.1 1.09276
wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558] Ranked 214.611 212.546 1.00972
1976 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] Squared 24782.4 27081.1 1.09276
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Rooted 63.6643 65.4435 1.02795
rest corepressor. [refseq;acc:nm_015156] Ranked 214.611 212.546 1.00972
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Measured 5939.85 6294.91 1.05978
1977 flotillin-1. [swissprot;acc:o75955] Squared 24782.4 27081.1 1.09276
homolog of yeast maf1. [refseq;acc:nm_032272] Ranked 209.539 207.529 1.00969
lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358] Measured 5782.86 6126.69 1.05946
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] Rooted 68.8473 70.77 1.02793
1978 sestrin 2 (hi95). [swissprot;acc:p58004] Squared 24782.4 27081.1 1.09276
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Rooted 62.1707 63.9068 1.02792
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Ranked 209.539 207.529 1.00969
uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Measured 5475.74 5800.97 1.05939
1979 26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998] Rooted 61.9542 63.6738 1.02776

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/