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 8291 to 8340 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2073 possible global transcription activator snf2l1. [swissprot;acc:p28370] Rooted 61.089 62.6862 1.02615
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Ranked 229.267 227.433 1.00806
2074 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Measured 3614.91 3423.89 1.05579
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Squared 34266.3 31445.7 1.0897
dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] Ranked 216.324 214.599 1.00804
tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981] Rooted 61.089 62.6862 1.02615
2075 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Ranked 221.703 223.483 1.00803
possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531] Rooted 61.089 62.6862 1.02615
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Measured 3614.91 3423.89 1.05579
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Squared 26521.6 28897.7 1.08959
2076 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). [swissprot;acc:p56377] 25481.8 27764.1 1.08957
af-6 protein. [swissprot;acc:p55196] Measured 5746.65 6067.27 1.05579
peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] Ranked 221.703 223.483 1.00803
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. [refseq;acc:nm_003075] Rooted 61.0883 62.6822 1.02609
2077 60s ribosomal protein l34. [swissprot;acc:p49207] Measured 3614.91 3423.89 1.05579
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). [swissprot;acc:q96pc3] Squared 25481.8 27764.1 1.08957
dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] Rooted 55.3465 53.9391 1.02609
iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Ranked 221.703 223.483 1.00803
2078 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). [swissprot;acc:q00382] Squared 25481.8 27764.1 1.08957
channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] Rooted 62.3035 63.9253 1.02603
fidgetin-like 1. [refseq;acc:nm_022116] Ranked 215.511 213.814 1.00794
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Measured 3614.91 3423.89 1.05579
2079 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). [swissprot;acc:q10567] Squared 25451.6 27731.3 1.08957
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] Ranked 215.967 214.28 1.00787
presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352] Rooted 62.3037 63.9256 1.02603
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Measured 3614.91 3423.89 1.05579
2080 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] Squared 25481.8 27764.1 1.08957
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Ranked 215.967 214.28 1.00787
presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796] Rooted 62.3037 63.9256 1.02603
r3h domain protein 1. [swissprot;acc:q15032] Measured 5837.34 6162.91 1.05577
2081 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). [swissprot;acc:o43747] Squared 25481.8 27764 1.08956
dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690] Ranked 215.967 214.28 1.00787
paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] Measured 6318.3 6670.1 1.05568
presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] Rooted 62.3021 63.9238 1.02603
2082 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 64.5014 66.1778 1.02599
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). [swissprot;acc:p21851] Squared 25510.2 27794.9 1.08956
phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] Ranked 215.967 214.28 1.00787
ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792] Measured 5800.93 6123.38 1.05559
2083 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] Squared 24238.8 26406.9 1.08945
enhancer of rudimentary homolog. [swissprot;acc:q14259] Rooted 64.5014 66.1778 1.02599
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Measured 5799.84 6122.18 1.05558
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Ranked 215.258 213.579 1.00786
2084 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] 222.548 224.293 1.00784
kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [refseq;acc:nm_003685] Rooted 62.2024 63.8123 1.02588
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062] Squared 18998.8 20695.9 1.08933
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Measured 5800.22 6122.6 1.05558
2085 channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] 5835.4 6159.4 1.05552
far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] Rooted 62.205 63.8126 1.02584
isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p50213] Ranked 222.58 224.32 1.00782
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Squared 24794.9 27009.7 1.08932

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/