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 2930 to 2979 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
733 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Measured 13241.4 11864 1.1161
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Rooted 52.0099 55.5904 1.06884
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] Squared 26029.1 30413.6 1.16845
734 loh1cr12. [refseq;acc:nm_058169] Rooted 57.805 61.7803 1.06877
presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] Ranked 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
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] Squared 26032.5 30417.7 1.16845
735 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] 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
unr protein. [swissprot;acc:o75534] Rooted 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
736 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Ranked 232.601 244.534 1.0513
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Squared 22017.1 25721.9 1.16827
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Measured 5768.32 6434.78 1.11554
wd-repeat protein 3. [swissprot;acc:q9unx4] Rooted 51.5438 55.0853 1.06871
737 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 5768.32 6434.78 1.11554
pnas-18. [sptrembl;acc:q9bzu3] Rooted 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
syntaxin 7. [swissprot;acc:o15400] Rooted 61.5022 65.7076 1.06838
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Squared 31467.1 36752.2 1.16796
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Ranked 222.825 211.966 1.05123
739 cellular modulator of immune recognition. [refseq;acc:nm_145021] Measured 5768.32 6434.78 1.11554
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Rooted 65.3677 69.828 1.06823
phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Ranked 223.58 235.027 1.0512
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Squared 25727.7 30046.7 1.16787
740 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] Ranked 223.58 235.027 1.0512
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Rooted 53.1114 56.7251 1.06804
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Squared 22075.1 25775.1 1.16761
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Measured 5768.32 6434.78 1.11554
741 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Rooted 53.1114 56.7251 1.06804
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Measured 5768.32 6434.78 1.11554
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Ranked 223.58 235.027 1.0512
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Squared 23894.7 27894.5 1.16739
742 brain protein 44. [swissprot;acc:o95563] Ranked 126.215 120.078 1.05111
eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Measured 4131.04 4607.9 1.11543
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Squared 31406.6 36662.8 1.16736
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Rooted 67.0234 71.5506 1.06755
743 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Squared 31406.6 36662.8 1.16736
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Measured 4131.04 4607.9 1.11543
katanin p60 subunit a 1. [refseq;acc:nm_007044] Rooted 54.4988 51.0573 1.0674
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Ranked 126.215 120.078 1.05111
744 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Squared 31406.6 36662.8 1.16736
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Measured 12515.4 11221.1 1.11535
dynactin 4. [refseq;acc:nm_032486] Rooted 55.2242 51.7372 1.0674
septin 6. [swissprot;acc:q14141] Ranked 126.604 120.463 1.05098
745 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Squared 31406.6 36662.8 1.16736
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Measured 4086.6 4557.68 1.11527
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Ranked 214.679 225.568 1.05072

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/