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 15930 to 15979 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1992 cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Squared Subtracted 24896.2 26952.9 2056.7
histone deacetylase 4 (hd4). [swissprot;acc:p56524] Rooted 61.3383 63.0785 1.7402
proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] Ranked 216.201 214.245 1.956
solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] Measured Divided 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
ubiquitin. [swissprot;acc:p02248] Measured Subtracted 7484.98 7821.11 336.13
zasp protein (fragment). [sptrembl;acc:q9y4z3] Ranked Divided 219.267 217.207 1.00948
1993 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] Squared Subtracted 24896.2 26952.9 2056.7
creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] Ranked 198.3 196.347 1.953
histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Rooted 61.3383 63.0785 1.7402
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Ranked Divided 189.052 190.835 1.00943
nucleoporin like 1. [refseq;acc:nm_014089] Measured 6174.74 6538.73 1.05895
rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Subtracted 5521.07 5856.93 335.86
seven in absentia homolog 1. [refseq;acc:nm_003031] Squared Divided 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 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Ranked Subtracted 198.293 196.341 1.952
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] Divided 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
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Measured Subtracted 6682.7 7018.29 335.59
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Divided 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
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Subtracted 15483.8 17529.5 2045.7
sorting nexin 5. [swissprot;acc:q9y5x3] Rooted 62.2844 60.5473 1.7371
1995 adaptor-related protein complex 1, mu 1 subunit (mu-adaptin 1) (adaptor protein complex ap-1 mu-1 subunit) (golgi adaptor ha1/ap1 adaptin mu-1 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 1) (clathrin coat assembly protein ap47) (clathrin coat associated protein ap47) (ap-mu chain family member mu1a). [swissprot;acc:q9bxs5] Measured 5684.61 6018.72 334.11
cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] Divided 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
peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] Ranked Subtracted 198.258 196.319 1.939
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 Divided 24786.9 27055.4 1.09152
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Rooted Subtracted 62.1707 63.9068 1.7361
zinc finger protein 277. [swissprot;acc:q9nrm2] Squared 15483.8 17529.5 2045.7
1996 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Rooted Divided 65.5898 67.3896 1.02744
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] Squared 24786.9 27055.5 1.09152
polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] Measured Subtracted 6024.47 6356.56 332.09
prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675] Ranked 198.258 196.319 1.939
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Divided 204.682 202.784 1.00936
splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] Rooted Subtracted 60.5071 62.2414 1.7343
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Measured Divided 5047.2 5344.68 1.05894
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] Squared Subtracted 33749 35794.2 2045.2
1997 60s ribosomal protein l26. [swissprot;acc:q02877] Divided 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
j domain protein c21orf55. [swissprot;acc:q9nx36] Ranked Subtracted 198.257 196.319 1.938
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Divided 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
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Squared Subtracted 23392.8 25437 2044.2
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] Measured 6024.47 6356.56 332.09
splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081] Rooted 60.5071 62.2414 1.7343
1998 adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] Measured 5671.62 6003.67 332.05
creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277] Ranked 198.19 196.252 1.938
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Rooted Divided 65.5918 67.3916 1.02744

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/