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 1660 to 1709 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
208 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Measured Subtracted 10599.9 12064.7 1464.8
cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Squared Divided 70525.9 52678.7 1.33879
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Ranked 285.684 252.234 1.13261
septin 10 isoform 1. [refseq;acc:nm_144710] Rooted Subtracted 113.733 123.871 10.138
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Measured Divided 4068.78 5082.18 1.24907
209 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Squared Subtracted 62757.7 50767.8 11989.9
brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Ranked 240.782 265.717 24.935
calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Rooted Divided 46.8525 53.5324 1.14257
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Squared 70525.9 52678.7 1.33879
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Ranked 285.684 252.234 1.13261
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Rooted Subtracted 121.695 131.815 10.12
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Measured 11383.2 9926.61 1456.59
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Divided 4068.78 5082.18 1.24907
210 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Squared Subtracted 36359.2 24466.8 11892.4
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Rooted Divided 46.8525 53.5316 1.14256
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Ranked 285.684 252.234 1.13261
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Rooted Subtracted 121.695 131.815 10.12
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Measured 4355.61 5810.82 1455.21
rna-binding protein. [refseq;acc:nm_019027] Ranked 237.302 212.41 24.892
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Squared Divided 69549 92953.5 1.33652
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Measured 4068.82 5082.21 1.24906
211 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Ranked Subtracted 237.302 212.41 24.892
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared 28994.2 17134.8 11859.4
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Rooted 121.695 131.815 10.12
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured 4358.13 5811.49 1453.36
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Rooted Divided 88.4361 77.5112 1.14095
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Squared 14668.3 19547 1.3326
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked 285.684 252.234 1.13261
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Measured 4068.91 5082.27 1.24905
212 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Rooted 88.4266 77.5047 1.14092
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Ranked 285.684 252.234 1.13261
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Rooted Subtracted 121.695 131.815 10.12
ns1-associated protein 1. [refseq;acc:nm_006372] Ranked 237.302 212.41 24.892
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Squared Divided 14690.3 19560.2 1.3315
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Subtracted 28994.2 17134.8 11859.4
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Measured Divided 4446.72 5553.79 1.24896
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Subtracted 6416.68 7865.15 1448.47
213 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Rooted Divided 105.205 92.2415 1.14054
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Squared Subtracted 28994.2 17134.8 11859.4
carboxypeptidase b precursor. [refseq;acc:nm_020361] Measured 7711.38 6265.8 1445.58
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Ranked 237.302 212.41 24.892
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Rooted 121.695 131.815 10.12
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Measured Divided 4446.72 5553.79 1.24896
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Ranked 210.693 186.95 1.127
signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Squared 86861.5 65369.7 1.32877
214 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Rooted Subtracted 121.695 131.815 10.12
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked Divided 191.644 170.192 1.12605
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Measured Subtracted 7711.36 6265.79 1445.57
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Ranked 241.282 266.12 24.838
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared 28994.2 17134.8 11859.4

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/