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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5858 to 5907 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
733 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Ranked Divided 164 155.961 1.05154
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Measured 13241.4 11864 1.1161
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Squared Subtracted 16442.8 20662.7 4219.9
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Rooted Divided 52.0099 55.5904 1.06884
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Ranked Subtracted 224.385 235.131 10.746
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Measured 5890.41 6547.81 657.4
Squared Divided 26029.1 30413.6 1.16845
734 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] Measured Subtracted 5890.59 6547.99 657.4
exocyst complex component sec15b. [swissprot;acc:q9y2d4] Rooted 62.5729 66.9286 4.3557
loh1cr12. [refseq;acc:nm_058169] Divided 57.805 61.7803 1.06877
polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] Ranked Subtracted 224.385 235.131 10.746
presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] Divided 232.601 244.534 1.0513
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Measured 13241.4 11864 1.1161
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Squared Subtracted 23947.4 28163.7 4216.3
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Divided 26032.5 30417.7 1.16845
735 40s ribosomal protein s5. [swissprot;acc:p46782] Rooted Subtracted 50.4649 46.1093 4.3556
acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Squared 23947.7 28163.9 4216.2
atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] Divided 26030.5 30415.2 1.16844
gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] Ranked 232.601 244.534 1.0513
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Subtracted 229.045 218.343 10.702
unr protein. [swissprot;acc:o75534] Rooted Divided 57.805 61.7803 1.06877
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Measured 5768.32 6434.78 1.11554
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Subtracted 5890.88 6548.28 657.4
736 exocyst complex component sec15a. [swissprot;acc:q8tag9] Rooted 62.5069 66.8603 4.3534
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Ranked Divided 232.601 244.534 1.0513
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Subtracted 228.78 218.091 10.689
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Squared Divided 22017.1 25721.9 1.16827
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Measured 5768.32 6434.78 1.11554
translation initiation factor if-2. [swissprot;acc:o60841] Subtracted 5811.51 6467.62 656.11
ubiquitin-like protein smt3a. [swissprot;acc:p55854] Squared 23948 28164.1 4216.1
wd-repeat protein 3. [swissprot;acc:q9unx4] Rooted Divided 51.5438 55.0853 1.06871
737 atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] Measured Subtracted 6000.07 6655.11 655.04
exocyst complex component sec15b. [swissprot;acc:q9y2d4] Ranked 221.968 211.326 10.642
golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] Measured Divided 5768.32 6434.78 1.11554
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Squared Subtracted 23969.3 28175.3 4206
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Rooted 50.3239 54.6658 4.3419
pnas-18. [sptrembl;acc:q9bzu3] Divided 97.8205 91.5467 1.06853
septin 10 isoform 1. [refseq;acc:nm_144710] Ranked 125.526 119.402 1.05129
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Squared 31479.4 36770.8 1.16809
738 delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Measured 5768.32 6434.78 1.11554
exocyst complex component sec15a. [swissprot;acc:q8tag9] Ranked Subtracted 222.138 211.503 10.635
jm1 protein. [refseq;acc:nm_014008] Rooted 61.5849 65.9155 4.3306
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Measured 5248.07 5901.72 653.65
syntaxin 7. [swissprot;acc:o15400] Rooted Divided 61.5022 65.7076 1.06838
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Squared 31467.1 36752.2 1.16796
tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Subtracted 26312 30514.1 4202.1
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Ranked Divided 222.825 211.966 1.05123
739 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Subtracted 272.878 283.472 10.594
cellular modulator of immune recognition. [refseq;acc:nm_145021] Measured Divided 5768.32 6434.78 1.11554
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Rooted 65.3677 69.828 1.06823

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/