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 10714 to 10763 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2177 elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Measured 5887.43 6187.82 1.05102
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Ranked 210.961 209.563 1.00667
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Squared 18927.7 17453.5 1.08446
2178 elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] Measured 5893.23 6193.33 1.05092
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Ranked 210.961 209.563 1.00667
lamin a/c (70 kda lamin). [swissprot;acc:p02545] Squared 28995.9 31443.3 1.08441
protein sck (fragment). [swissprot;acc:p98077] Rooted 60.8609 62.2517 1.02285
2179 centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] Squared 28996.8 31444 1.0844
elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] Measured 5896.51 6196.59 1.05089
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Ranked 210.961 209.563 1.00667
heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626] Rooted 60.8609 62.2517 1.02285
2180 centaurin beta 2 (cnt-b2). [swissprot;acc:q15057] Squared 28996.7 31444 1.0844
elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926] Measured 5900.25 6200.24 1.05084
heat shock cognate 71 kda protein. [swissprot;acc:p11142] Ranked 210.961 209.563 1.00667
ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830] Rooted 60.8609 62.2517 1.02285
2181 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] Ranked 227.117 225.62 1.00664
centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] Squared 28996.8 31444 1.0844
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Measured 4915.05 5164.75 1.0508
2182 cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879] 5875.13 6173.41 1.05077
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Squared 22803.2 24727.6 1.08439
solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [swissprot;acc:q9ugh3] Rooted 60.8609 62.2517 1.02285
twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] Ranked 218.062 216.624 1.00664
2183 cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561] Measured 5875.11 6173.39 1.05077
dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [swissprot;acc:o14733] Rooted 60.8609 62.2517 1.02285
lamin b1. [swissprot;acc:p20700] Squared 28997.5 31444.7 1.08439
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Ranked 218.062 216.624 1.00664
2184 atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] Squared 23118.2 25068.9 1.08438
ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Rooted 60.8787 62.269 1.02284
rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Measured 5838.01 6132.35 1.05042
suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Ranked 211.713 210.318 1.00663
2185 60s ribosomal protein l12. [swissprot;acc:p30050] Measured 3586.32 3414.42 1.05035
bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933] Ranked 211.713 210.318 1.00663
fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] Squared 27346 29649.9 1.08425
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Rooted 60.8787 62.269 1.02284
2186 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Measured 3586.3 3414.4 1.05035
fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469] Squared 27346 29649.9 1.08425
glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Ranked 211.713 210.318 1.00663
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Rooted 71.1486 72.7731 1.02283
2187 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Measured 3586.31 3414.41 1.05035
fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Squared 27346 29649.9 1.08425
glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Ranked 211.713 210.318 1.00663
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Rooted 60.0718 61.4379 1.02274
2188 glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 66.6512 68.1643 1.0227
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Measured 6682.7 7018.29 1.05022
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Ranked 209.54 208.162 1.00662
wd-repeat protein 4. [swissprot;acc:p57081] Squared 27346 29649.9 1.08425
2189 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Ranked 209.54 208.162 1.00662
bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] Squared 23062.1 25005.1 1.08425
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Measured 5285.03 5033.55 1.04996

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/