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 1680 to 1729 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
210 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Measured Divided 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
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Rooted Divided 105.205 92.2415 1.14054
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Squared 52591.3 69845.1 1.32807
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Measured 4074.83 5086.49 1.24827
215 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Rooted 105.205 92.2415 1.14054
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked Subtracted 237.292 212.457 24.835
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Rooted 121.695 131.815 10.12
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Ranked Divided 112 126 1.125
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 Subtracted 7711.31 6265.76 1445.55
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 28994.2 17134.8 11859.4
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Divided 86609.4 65234.5 1.32766
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Measured 16074 12888.4 1.24717
216 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Subtracted 10067.9 11511 1443.1
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Rooted 121.695 131.815 10.12
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Squared 46785.7 58383.2 11597.5
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Measured Divided 16071.6 12886.8 1.24714
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Ranked 112 126 1.125
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Rooted 105.205 92.2415 1.14054
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Squared 86600.9 65229.9 1.32763
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Ranked Subtracted 226.471 201.769 24.702
217 60s ribosomal protein l26. [swissprot;acc:q02877] 242.326 267.008 24.682

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/