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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6991 to 7040 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
874 UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Squared Subtracted 15588.1 19381.8 3793.7
ZNF274 zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Ranked 269.953 278.215 8.262
875 ADSL adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Squared 33294.4 37086.4 3792
CHRNA6 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Rooted Divided 84.6378 89.8201 1.06123
ESRRB steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Measured 10263.8 11318.6 1.10277
HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Rooted Subtracted 69.5394 73.3277 3.7883
JUP junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Ranked 223.906 215.653 8.253
NDUFS6 nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380] Squared Divided 18650.4 21632 1.15987
PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Ranked 212.002 203.954 1.03946
PRODH2 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Measured Subtracted 6604.44 7183.07 578.63
876 no value tax interaction protein 1. [refseq;acc:nm_014604] Ranked 223.906 215.653 8.253
CROT peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Measured Divided 5644.68 6223.23 1.10249
HIVEP1 zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Rooted Subtracted 69.5394 73.3277 3.7883
ISCU nitrogen fixation cluster-like. [refseq;acc:nm_014301] Divided 84.6378 89.8201 1.06123
MYL6 myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] Squared 18650.4 21632 1.15987
PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Ranked 212.002 203.954 1.03946
RNF25 ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Measured Subtracted 9946.21 9367.66 578.55
SPTLC2 serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] Squared 24804.6 28595.4 3790.8
877 no value myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Divided 18650.4 21632 1.15987
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Subtracted 27802.5 31577 3774.5
CROT peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Measured 5644.68 6223.23 578.55
HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Rooted 69.5394 73.3277 3.7883
MAD2L2 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Measured Divided 5797.88 6391.75 1.10243
PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Ranked 212.002 203.954 1.03946
STARD13 star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Rooted 84.6378 89.8201 1.06123
ZNF444 zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Ranked Subtracted 269.896 278.093 8.197
878 no value mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Measured Divided 5797.88 6391.75 1.10243
CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Rooted Subtracted 74.1383 77.9257 3.7874
LIPF triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Squared Divided 23242.1 26955.1 1.15975
NAV2 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Subtracted 29909.9 33684.3 3774.4
PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Ranked Divided 212.002 203.954 1.03946
SLC5A5 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Measured Subtracted 6600.36 7178.84 578.48
STARD8 star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Rooted Divided 84.6378 89.8201 1.06123
STX7 syntaxin 7. [swissprot;acc:o15400] Ranked Subtracted 217.181 209.012 8.169
879 CHRNA2 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Rooted Divided 84.6378 89.8201 1.06123
FARSA phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Ranked Subtracted 217.491 209.323 8.168
GALK2 n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Rooted 59.7298 63.5169 3.7871
IPO11 ran binding protein 11. [refseq;acc:nm_016338] Measured 6138.91 6717.05 578.14
LIPM ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] Squared Divided 23242.1 26955.1 1.15975
NUP88 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Measured 5797.88 6391.75 1.10243
PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Ranked 212.002 203.954 1.03946
PTPN2 protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] Squared Subtracted 27784.4 31556.6 3772.2
880 no value galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Rooted 59.7298 63.5169 3.7871
FAM57A membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Measured 6136.99 6714.98 577.99
FARS2 phenylalanine-trna synthetase. [refseq;acc:nm_006567] Ranked 217.491 209.323 8.168
LIPA lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Squared Divided 23242.1 26955.1 1.15975
MAPKAPK3 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Rooted 84.6378 89.8201 1.06123
MTRF1 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Measured 5166.04 5694.55 1.1023
NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Squared Subtracted 29911.6 33682.9 3771.3
PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Ranked Divided 212.002 203.954 1.03946

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
- Hugo is the HGNC identifier if it exists
- 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/