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.


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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 7936 to 7985 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1984 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Measured 5830.03 6176.1 1.05936
1985 importin 4. [refseq;acc:nm_024658] Rooted 60.943 62.6188 1.0275
limkain beta 2. [refseq;acc:nm_025140] Squared 26689.4 29149.1 1.09216
mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] Ranked 219.26 217.193 1.00952
scribble. [refseq;acc:nm_015356] Measured 5516.89 5844.37 1.05936
1986 65 kda yes-associated protein (yap65). [swissprot;acc:p46937] Ranked 219.26 217.193 1.00952
lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214] Measured 5517.24 5844.68 1.05935
methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Squared 31643.5 34556.7 1.09206
serpin b12. [swissprot;acc:q96p63] Rooted 61.8616 63.5621 1.02749
1987 lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] Ranked 225.022 222.9 1.00952
megsin (tp55) (serpin b7). [swissprot;acc:o75635] Rooted 61.8616 63.5621 1.02749
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] Measured 5829.74 6175.69 1.05934
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Squared 14837.7 16203.5 1.09205
1988 9 kda protein. [swissprot;acc:p13994] Ranked 219.26 217.193 1.00952
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Rooted 61.8616 63.5621 1.02749
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Measured 3559.49 3360.39 1.05925
seven in absentia homolog 2. [refseq;acc:nm_005067] Squared 24151.6 26364.8 1.09164
1989 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 12388.6 13523.5 1.09161
collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] Ranked 219.261 217.195 1.00951
m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] Measured 4383.34 4642.93 1.05922
oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055] Rooted 61.8616 63.5621 1.02749
1990 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Ranked 219.26 217.194 1.00951
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Squared 12388.6 13523.5 1.09161
transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] Measured 5045.67 5344.06 1.05914
upf0183 protein. [swissprot;acc:q9bsu1] Rooted 61.8616 63.5621 1.02749
1991 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] Squared 24134.9 26345.3 1.09159
solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] Measured 5429.27 5749.69 1.05902
transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] Ranked 219.26 217.194 1.00951
1992 60s ribosomal protein l35. [swissprot;acc:p42766] Squared 12384 13518 1.09157
solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] Measured 5429.27 5749.69 1.05902
translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Rooted 61.8616 63.5621 1.02749
zasp protein (fragment). [sptrembl;acc:q9y4z3] Ranked 219.267 217.207 1.00948
1993 huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 189.052 190.835 1.00943
nucleoporin like 1. [refseq;acc:nm_014089] Measured 6174.74 6538.73 1.05895
seven in absentia homolog 1. [refseq;acc:nm_003031] Squared 24121.1 26329.1 1.09154
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] Rooted 61.8616 63.5621 1.02749
1994 goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Ranked 189.011 190.787 1.0094
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Rooted 61.8616 63.5621 1.02749
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Measured 6174.74 6538.73 1.05895
serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209] Squared 24786.8 27055.9 1.09154
1995 cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] Measured 6174.74 6538.73 1.05895
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Ranked 188.961 190.73 1.00936
isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Rooted 74.6532 76.7018 1.02744
serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] Squared 24786.9 27055.4 1.09152
1996 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Rooted 65.5898 67.3896 1.02744
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] Squared 24786.9 27055.5 1.09152
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Ranked 204.682 202.784 1.00936
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Measured 5047.2 5344.68 1.05894
1997 60s ribosomal protein l26. [swissprot;acc:q02877] Squared 12380.1 13513 1.09151

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/