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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 943 to 992 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
236 STARD13 Squared star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] 42411.6 55802.1 1.31573
TXNL4A Measured spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 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 Rooted melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 137.446 120.823 1.13758
STARD8 Squared star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] 42411.6 55802.1 1.31573
STX18 Ranked syntaxin 18. [swissprot;acc:q9p2w9] 227.357 254.15 1.11785
238 no value rd protein. [swissprot;acc:p18615]
CHRNA2 Squared neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 42411.6 55802.1 1.31573
MAGEA4 Rooted melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 137.446 120.823 1.13758
PPP1R7 Measured protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 27642.5 22440.4 1.23182
239 no value Rooted melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 137.446 120.823 1.13758
CPA6 Measured carboxypeptidase b precursor. [refseq;acc:nm_020361] 7711.38 6265.8 1.23071
GSTO1 Ranked glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 227.357 254.15 1.11785
MAPKAPK3 Squared mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 42411.6 55802.1 1.31573
240 AIG1 Ranked androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 227.357 254.15 1.11785
CPA3 Measured mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 7711.36 6265.79 1.23071
MAGEA10 Rooted melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 137.446 120.823 1.13758
MAPK14 Squared 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] 42411.6 55802.1 1.31573
241 ATP5F1 Ranked atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 227.357 254.15 1.11785
CHRNA4 Squared neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 42411.6 55802.1 1.31573
CPB2 Measured plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 7711.31 6265.76 1.23071
MAGEB4 Rooted melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 137.446 120.823 1.13758
242 CHRNA3 Squared neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 42411.6 55802.1 1.31573
DNAJC12 Ranked j domain containing protein 1. [swissprot;acc:q9ukb3] 227.357 254.15 1.11785
MAGED2 Rooted 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] 137.446 120.823 1.13758
MAX Measured max protein. [swissprot;acc:p25912] 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 Ranked sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 227.357 254.15 1.11785
SPHK2 Squared sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 42411.6 55802.1 1.31573
TRO Rooted trophinin. [swissprot;acc:q12816] 137.446 120.823 1.13758
244 COQ7 Measured ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 4250.14 5211.25 1.22614
GSTO2 Ranked ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 227.357 254.15 1.11785
MYO5B Rooted myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 146.94 167.046 1.13683
NCBP2L Squared dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 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 Measured homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 4251.65 5212.33 1.22595
MYO5C Rooted myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 146.94 167.046 1.13683
SNRPD3 Ranked small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 226.109 202.333 1.11751
246 no value Rooted myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 146.94 167.046 1.13683
EIF4G3 Ranked eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 212.363 1.11748
HOMER3 Measured homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 4252.66 5213.05 1.22583
PYGB Squared glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 8875.01 6768.05 1.31131
247 no value Ranked rna-binding protein. [refseq;acc:nm_019027] 237.302 212.41 1.11719
DDX56 Rooted probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 47.3621 53.8355 1.13668
PYGL Squared glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 8875.01 6768.05 1.31131
WAS Measured wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 6416.68 7865.15 1.22574
248 no value Ranked apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 237.302 212.41 1.11719
CRK Measured proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 6417.18 7859.6 1.22477
LSM5 Rooted u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 56.0466 63.4808 1.13264
MYO15A Squared myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 8875.01 6768.05 1.31131

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/