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 936 to 985 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
234 RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Measured 5181.2 6410.58 1.23728
235 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
ISCU nitrogen fixation cluster-like. [refseq;acc:nm_014301] Squared 42411.6 55802.1 1.31573
MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Rooted 137.446 120.823 1.13758
PAH phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Ranked 227.357 254.15 1.11785
236 DUS1L pp3111 protein. [refseq;acc:nm_022156]
MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Rooted 137.446 120.823 1.13758
STARD13 star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Squared 42411.6 55802.1 1.31573
TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Measured 4723.53 5828.46 1.23392
237 LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 4567.04 5631.2 1.23301
MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Rooted 137.446 120.823 1.13758
STARD8 star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Squared 42411.6 55802.1 1.31573
STX18 syntaxin 18. [swissprot;acc:q9p2w9] Ranked 227.357 254.15 1.11785
238 no value rd protein. [swissprot;acc:p18615]
CHRNA2 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Squared 42411.6 55802.1 1.31573
MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Rooted 137.446 120.823 1.13758
PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Measured 27642.5 22440.4 1.23182
239 no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Rooted 137.446 120.823 1.13758
CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] Measured 7711.38 6265.8 1.23071
GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Ranked 227.357 254.15 1.11785
MAPKAPK3 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Squared 42411.6 55802.1 1.31573
240 AIG1 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Ranked 227.357 254.15 1.11785
CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Measured 7711.36 6265.79 1.23071
MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Rooted 137.446 120.823 1.13758
MAPK14 mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Squared 42411.6 55802.1 1.31573
241 ATP5F1 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Ranked 227.357 254.15 1.11785
CHRNA4 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Squared 42411.6 55802.1 1.31573
CPB2 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Measured 7711.31 6265.76 1.23071
MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Rooted 137.446 120.823 1.13758
242 CHRNA3 neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Squared 42411.6 55802.1 1.31573
DNAJC12 j domain containing protein 1. [swissprot;acc:q9ukb3] Ranked 227.357 254.15 1.11785
MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Rooted 137.446 120.823 1.13758
MAX max protein. [swissprot;acc:p25912] Measured 4640.26 5704.87 1.22943
243 HOMER2 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 4246.95 5208.98 1.22652
SNX13 sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Ranked 227.357 254.15 1.11785
SPHK2 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Squared 42411.6 55802.1 1.31573
TRO trophinin. [swissprot;acc:q12816] Rooted 137.446 120.823 1.13758
244 COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Measured 4250.14 5211.25 1.22614
GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Ranked 227.357 254.15 1.11785
MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Rooted 146.94 167.046 1.13683
NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Squared 14728.8 19330.8 1.31245
245 GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 8875.01 6768.05 1.31131
HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Measured 4251.65 5212.33 1.22595
MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Rooted 146.94 167.046 1.13683
SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Ranked 226.109 202.333 1.11751
246 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Rooted 146.94 167.046 1.13683
EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Ranked 237.312 212.363 1.11748
HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Measured 4252.66 5213.05 1.22583
PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Squared 8875.01 6768.05 1.31131
247 no value rna-binding protein. [refseq;acc:nm_019027] Ranked 237.302 212.41 1.11719

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/