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.


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 9114 to 9163 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2279 solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Rooted 62.0161 60.7934 1.02011
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Ranked 191.936 190.909 1.00538
ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Measured 5783.73 6048.91 1.04585
2280 nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] Squared 28792.5 31087.2 1.0797
proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] Ranked 212.793 211.657 1.00537
rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156] Measured 5783.73 6048.91 1.04585
translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] Rooted 60.1708 61.3807 1.02011
2281 adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326] Squared 30412.1 32833.7 1.07963
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] Rooted 59.0309 60.2133 1.02003
polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] Measured 5783.73 6048.91 1.04585
splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] Ranked 219.652 218.482 1.00536
2282 adaptor-associated kinase 1. [refseq;acc:nm_014911] Measured 5783.73 6048.91 1.04585
dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Rooted 59.0309 60.2133 1.02003
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6] Squared 27002.8 29139.5 1.07913
splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081] Ranked 219.652 218.482 1.00536
2283 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Measured 5783.7 6048.88 1.04585
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Rooted 88.734 87.0008 1.01992
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] Squared 29812 32162.2 1.07883
proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] Ranked 212.81 211.676 1.00536
2284 dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Measured 5783.73 6048.91 1.04585
itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Squared 29812 32162.2 1.07883
p28 ing5. [refseq;acc:nm_032329] Rooted 62.3469 63.5849 1.01986
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Ranked 219.652 218.482 1.00536
2285 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Squared 8157.62 8800.59 1.07882
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Rooted 88.6852 86.9598 1.01984
rho-gtpase activating protein 10. [refseq;acc:nm_020824] Measured 5783.73 6048.91 1.04585
splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368] Ranked 219.652 218.482 1.00536
2286 dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] 216.608 215.456 1.00535
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Rooted 60.3647 61.5614 1.01982
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Measured 5783.76 6048.94 1.04585
translin. [swissprot;acc:q15631] Squared 20372 21974.2 1.07865
2287 glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Rooted 63.0728 64.3156 1.0197
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] Ranked 206.475 205.376 1.00535
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Measured 5783.7 6048.88 1.04585
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Squared 20372 21974.2 1.07865
2288 2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] Measured 5783.76 6048.94 1.04585
dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Ranked 216.607 215.458 1.00533
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Rooted 63.0728 64.3156 1.0197
polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] Squared 20372 21974.2 1.07865
2289 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Rooted 63.0728 64.3156 1.0197
ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] Measured 5783.76 6048.94 1.04585
dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Ranked 216.605 215.46 1.00531
regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] Squared 26044.4 28086.9 1.07842
2290 calmegin precursor. [swissprot;acc:o14967] 27825.3 30004.3 1.07831
metaxin 2. [swissprot;acc:o75431] Rooted 65.3922 64.1376 1.01956
myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] Ranked 200.158 201.213 1.00527
phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Measured 5783.75 6048.93 1.04585
2291 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Ranked 200.158 201.213 1.00527
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] Squared 27825.3 30004.3 1.07831
clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Measured 5783.71 6048.89 1.04585

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/