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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 1680 to 1729 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
Value Type
network_comparison
red
green
210 Subtracted LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Measured 1455.21 4355.61 5810.82
211 Divided CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 1.24905 4068.91 5082.27
PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Rooted 1.14095 88.4361 77.5112
PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked 1.13261 285.684 252.234
TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Squared 1.3326 14668.3 19547
Subtracted no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Ranked 24.892 237.302 212.41
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Rooted 10.12 121.695 131.815
LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured 1453.36 4358.13 5811.49
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared 11859.4 28994.2 17134.8
212 Divided ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Rooted 1.14092 88.4266 77.5047
BRF1 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 1.24896 4446.72 5553.79
CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Ranked 1.13261 285.684 252.234
TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Squared 1.3315 14690.3 19560.2
Subtracted no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Rooted 10.12 121.695 131.815
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Squared 11859.4 28994.2 17134.8
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Ranked 24.892 237.302 212.41
WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Measured 1448.47 6416.68 7865.15
213 Divided NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 1.24896 4446.72 5553.79
PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Ranked 1.127 210.693 186.95
STAM signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Squared 1.32877 86861.5 65369.7
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Rooted 1.14054 105.205 92.2415
Subtracted CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] Measured 1445.58 7711.38 6265.8
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Ranked 24.892 237.302 212.41
HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Rooted 10.12 121.695 131.815
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Squared 11859.4 28994.2 17134.8
214 Divided CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Measured 1.24827 4074.83 5086.49
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Rooted 1.14054 105.205 92.2415
LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked 1.12605 191.644 170.192
TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Squared 1.32807 52591.3 69845.1
Subtracted CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Measured 1445.57 7711.36 6265.79
HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Rooted 10.12 121.695 131.815
MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Ranked 24.838 241.282 266.12
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared 11859.4 28994.2 17134.8
215 Divided no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Ranked 1.125 112 126
KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Measured 1.24717 16074 12888.4
PRKCH protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Squared 1.32766 86609.4 65234.5
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Rooted 1.14054 105.205 92.2415
Subtracted CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 11859.4 28994.2 17134.8
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 1445.55 7711.31 6265.76
EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked 24.835 237.292 212.457
HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Rooted 10.12 121.695 131.815
216 Divided MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Ranked 1.125 112 126
PRKCE protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Squared 1.32763 86600.9 65229.9
SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Measured 1.24714 16071.6 12886.8
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Rooted 1.14054 105.205 92.2415
Subtracted no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 10.12 121.695 131.815
ECHS1 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Measured 1443.1 10067.9 11511
RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Squared 11597.5 46785.7 58383.2
SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Ranked 24.702 226.471 201.769
217 Divided no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Measured 1.24714 16071.6 12886.8

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/