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 3708 to 3757 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
927 vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Rooted 62.0422 65.7019 1.05899
928 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Measured 5638.46 6194.04 1.09853
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Rooted 62.0422 65.7019 1.05899
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Ranked 225.976 218.017 1.03651
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Squared 20685.1 23904.8 1.15565
929 mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Ranked 225.955 218.015 1.03642
surfeit locus protein 1. [swissprot;acc:q15526] Measured 5638.46 6194.04 1.09853
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Squared 22626.3 26143 1.15543
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Rooted 62.3617 66.0327 1.05887
930 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Measured 5638.65 6194.23 1.09853
homolog of yeast maf1. [refseq;acc:nm_032272] Squared 26029.5 30074.5 1.1554
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Ranked 231.357 239.778 1.0364
931 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 159.13 164.917 1.03637
sec13-related protein. [swissprot;acc:p55735] Rooted 62.3618 66.0328 1.05887
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Measured 5638.59 6194.17 1.09853
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Squared 26029.5 30074.5 1.1554
932 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Measured 5638.46 6194.04 1.09853
mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Ranked 225.939 218.013 1.03636
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Squared 26029.5 30074.5 1.1554
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Rooted 62.3617 66.0327 1.05887
933 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Ranked 159.165 164.951 1.03635
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Measured 5638.46 6194.04 1.09853
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Squared 26029.5 30074.5 1.1554
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 62.3618 66.0328 1.05887
934 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] Squared 26029.5 30074.5 1.1554
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Ranked 242.024 233.544 1.03631
yeast sec31p homolog. [refseq;acc:nm_014933] Rooted 62.3618 66.0328 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 5640 6195.52 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 15461.1 17854.3 1.15479
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Measured 5413.63 5946.46 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 232.473 224.372 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 62.3617 66.0327 1.05887
936 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] Ranked 232.473 224.372 1.03611
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Measured 5628.21 6180.37 1.09811
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Squared 15461.1 17854.3 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 62.3618 66.0328 1.05887
937 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Squared 25043.9 28914 1.15453
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Measured 5859.25 6432.03 1.09776
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Ranked 220.246 212.618 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 62.3588 66.0297 1.05887
938 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Measured 5859.25 6432.03 1.09776
ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Rooted 62.3618 66.0328 1.05887
glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Squared 25043.4 28913.4 1.15453
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Ranked 220.246 212.618 1.03588
939 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 216.501 224.27
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Rooted 62.3617 66.0327 1.05887
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Squared 25044.9 28915.2 1.15453
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Measured 5859.25 6432.03 1.09776
940 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 5568.96 6113.35 1.09775

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/