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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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 Value Type description 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
Value Type
description
red
green
network_comparison
733 Ranked acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 164 155.961 1.05154
Squared 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] 26029.1 30413.6 1.16845
Rooted nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] 52.0099 55.5904 1.06884
734 Measured 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] 13241.4 11864 1.1161
Ranked presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] 232.601 244.534 1.0513
Squared 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] 26032.5 30417.7 1.16845
Rooted loh1cr12. [refseq;acc:nm_058169] 57.805 61.7803 1.06877
735 Measured vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] 5768.32 6434.78 1.11554
Ranked gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] 232.601 244.534 1.0513
Squared 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
Rooted unr protein. [swissprot;acc:o75534] 57.805 61.7803 1.06877
736 Measured sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] 5768.32 6434.78 1.11554
Ranked presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 232.601 244.534 1.0513
Squared putative sialoglycoprotease type 2. [refseq;acc:nm_022353] 22017.1 25721.9 1.16827
Rooted wd-repeat protein 3. [swissprot;acc:q9unx4] 51.5438 55.0853 1.06871
737 Measured 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] 5768.32 6434.78 1.11554
Ranked septin 10 isoform 1. [refseq;acc:nm_144710] 125.526 119.402 1.05129
Squared transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] 31479.4 36770.8 1.16809
Rooted pnas-18. [sptrembl;acc:q9bzu3] 97.8205 91.5467 1.06853
738 Measured delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] 5768.32 6434.78 1.11554
Ranked xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 222.825 211.966 1.05123
Squared transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 31467.1 36752.2 1.16796
Rooted syntaxin 7. [swissprot;acc:o15400] 61.5022 65.7076 1.06838
739 Measured cellular modulator of immune recognition. [refseq;acc:nm_145021] 5768.32 6434.78 1.11554
Ranked phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] 223.58 235.027 1.0512
Squared ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] 25727.7 30046.7 1.16787
Rooted exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] 65.3677 69.828 1.06823
740 Measured vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] 5768.32 6434.78 1.11554
Ranked 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] 223.58 235.027 1.0512
Squared o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] 22075.1 25775.1 1.16761
Rooted casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 53.1114 56.7251 1.06804
741 Measured gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] 5768.32 6434.78 1.11554
Ranked 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] 223.58 235.027 1.0512
Squared nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 23894.7 27894.5 1.16739
Rooted casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 53.1114 56.7251 1.06804
742 Measured eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 4131.04 4607.9 1.11543
Ranked brain protein 44. [swissprot;acc:o95563] 126.215 120.078 1.05111
Squared homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] 31406.6 36662.8 1.16736
Rooted transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 67.0234 71.5506 1.06755
743 Measured eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] 4131.04 4607.9 1.11543
Ranked septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 126.215 120.078 1.05111
Squared cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] 31406.6 36662.8 1.16736
Rooted katanin p60 subunit a 1. [refseq;acc:nm_007044] 54.4988 51.0573 1.0674
744 Measured cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 12515.4 11221.1 1.11535
Ranked septin 6. [swissprot;acc:q14141] 126.604 120.463 1.05098
Squared activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] 31406.6 36662.8 1.16736
Rooted dynactin 4. [refseq;acc:nm_032486] 55.2242 51.7372 1.0674
745 Measured neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 4086.6 4557.68 1.11527
Ranked solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] 214.679 225.568 1.05072
Squared cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] 31406.6 36662.8 1.16736

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/