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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 Interaction Map Value Type Network Comparison Type Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 3732 to 3781 of 12912 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
green
red
network_comparison
933 vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] Rooted 66.0328 62.3618 1.05887
934 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] Squared 30074.5 26029.5 1.1554
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Ranked 233.544 242.024 1.03631
yeast sec31p homolog. [refseq;acc:nm_014933] Rooted 66.0328 62.3618 1.05887
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Measured 6195.52 5640 1.0985
935 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Squared 17854.3 15461.1 1.15479
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Measured 5946.46 5413.63 1.09842
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Ranked 224.372 232.473 1.03611
vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] Rooted 66.0327 62.3617 1.05887
936 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] Ranked 224.372 232.473 1.03611
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Measured 6180.37 5628.21 1.09811
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Squared 17854.3 15461.1 1.15479
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] Rooted 66.0328 62.3618 1.05887
937 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Squared 28914 25043.9 1.15453
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Measured 6432.03 5859.25 1.09776
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Ranked 212.618 220.246 1.03588
vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] Rooted 66.0297 62.3588 1.05887
938 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Measured 6432.03 5859.25 1.09776
ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Rooted 66.0328 62.3618 1.05887
glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Squared 28913.4 25043.4 1.15453
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Ranked 212.618 220.246 1.03588
939 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 224.27 216.501
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Rooted 66.0327 62.3617 1.05887
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Squared 28915.2 25044.9 1.15453
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Measured 6432.03 5859.25 1.09776
940 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 6113.35 5568.96 1.09775
calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Ranked 205.088 212.442 1.03586
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Rooted 66.0328 62.3618 1.05887
glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] Squared 28986.7 25108.4 1.15446
941 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 30020.3 26005.2 1.1544
caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] Measured 5455.34 4970.21 1.09761
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Ranked 205.083 212.437 1.03586
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] Rooted 66.0328 62.3618 1.05887
942 cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] Squared 27312.6 23659.9 1.15438
grancalcin. [swissprot;acc:p28676] Ranked 205.088 212.442 1.03586
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Measured 7240.64 6597.56 1.09747
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Rooted 66.0328 62.3618 1.05887
943 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] Squared 27311.3 23659.2 1.15436
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Measured 7241 6597.98 1.09746
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Ranked 205.087 212.442 1.03586
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Rooted 66.0327 62.3617 1.05887
944 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Measured 7241 6597.98 1.09746
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Ranked 205.083 212.437 1.03586
tcd37 homolog; prune. [refseq;acc:nm_021222] Squared 27311.1 23659.1 1.15436
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Rooted 66.0323 62.3614 1.05886
945 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Measured 7241 6597.98 1.09746
brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Ranked 205.085 212.44 1.03586
cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] Squared 27310.2 23658.7 1.15434
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Rooted 66.0815 62.409 1.05885
946 cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] Squared 27309.8 23658.5 1.15433

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/