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 7964 to 8013 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1991 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
glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Rooted 65.5888 67.3886 1.02744
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Ranked 204.651 202.759 1.00933
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Measured 5047.2 5344.68 1.05894
1998 glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Rooted 65.5918 67.3916 1.02744
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Measured 5047.2 5344.68 1.05894
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Ranked 200.219 198.37 1.00932
serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454] Squared 24786.9 27055.2 1.09151
1999 60s ribosomal protein l3-like. [swissprot;acc:q92901] 12491.1 13633.8 1.09148
nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426] Measured 5047.2 5344.68 1.05894
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Ranked 204.636 202.748 1.00931
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] Rooted 63.242 64.9748 1.0274
2000 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 59.3823 61.0094
fidgetin-like 1. [refseq;acc:nm_022116] Squared 28497.2 31100 1.09134
ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153] Measured 5047.2 5344.68 1.05894
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Ranked 204.626 202.739 1.00931
2001 dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992] Measured 5047.2 5344.68 1.05894
lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] Ranked 225.02 222.948 1.00929
proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] Squared 29586.9 32287.8 1.09129
zinc finger protein 258. [refseq;acc:nm_145310] Rooted 59.3823 61.0094 1.0274
2002 dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Squared 14935 16296.6 1.09117
survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893] Measured 5047.2 5344.68 1.05894
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Ranked 214.775 216.769 1.00928
zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202] Rooted 59.3823 61.0094 1.0274
2003 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Squared 12429.9 13562.6 1.09113
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Ranked 208.315 206.41 1.00923
probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6] Measured 5047.2 5344.68 1.05894
zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095] Rooted 59.3823 61.0094 1.0274
2004 actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]

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/