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 65874 to 65923 of 66312 in total
Interaction Map  : Low confidence
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
red
green
network_comparison
5007 CTPS Measured ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Divided 9134.61 9127.55 1.00077
NR2C2 Rooted orphan nuclear receptor tr4 (orphan nuclear receptor tak1). [swissprot;acc:p49116] Subtracted 68.9664 69.0635 0.0971
PFDN2 Squared prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Divided 45539.2 45518.6 1.00045
Subtracted 20.6
PFKFB2 Rooted 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (6pf-2-k/fru- 2,6-p2ase heart-type isozyme) (pfk-2/fbpase-2) [includes: 6- phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:o60825] Divided 76.3109 76.4154 1.00137
TNRC6A Ranked trinucleotide repeat containing 6; edie; gw182 autoantigen. [refseq;acc:nm_014494] 208.596 208.556 1.00019
Subtracted 0.04
5008 ABI2 Measured abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] Divided 8608.57 8615.12 1.00076
CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Subtracted 9142.82 9136.28 6.54
PFKFB4 Rooted 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (6pf-2-k/fru- 2,6-p2ase testis-type isozyme) [includes: 6-phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:q16877] Divided 76.3109 76.4154 1.00137
RB1CC1 Ranked rb1-inducible coiled coil protein 1. [refseq;acc:nm_014781] 208.596 208.556 1.00019
Subtracted 0.04
SNAP29 Rooted synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] 68.9664 69.0635 0.0971
UXT Squared uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Divided 45539.2 45518.6 1.00045
Subtracted 20.6
5009 GMPPA Rooted gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Divided 82.9689 82.8676 1.00122
GNG10 Squared guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 40807.9 40792.8 1.00037
Subtracted 15.1
MRC1L1 Ranked macrophage mannose receptor precursor (mmr) (cd206 antigen). [swissprot;acc:p22897] Divided 205.102 205.132 1.00015
NEK1 serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Subtracted 205.104 205.135 0.031
RABEPK Measured rab9 effector p40. [refseq;acc:nm_005833] Divided 8545.09 8538.63 1.00076
Subtracted 6.46
SLC35E1 Rooted solute carrier family 35, member e1. [refseq;acc:nm_024881] 69.0363 68.9412 0.0951
5010 no value Squared repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Divided 47199.9 47185.2 1.00031
Subtracted 14.7
CTPS2 Measured cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Divided 9142.82 9136.28 1.00072
MRC1L1 Ranked macrophage mannose receptor precursor (mmr) (cd206 antigen). [swissprot;acc:p22897] Subtracted 205.102 205.132 0.03
PHKG2 Measured phosphorylase b kinase gamma catalytic chain, testis/liver isoform (ec 2.7.1.38) (phk-gamma-t) (phosphorylase kinase gamma subunit 2) (psk-c3). [swissprot;acc:p15735] 6658.39 6653.12 5.27
PLA2R1 Ranked phospholipase a2 receptor 1, 180kda; phospholipase a2 receptor 1, 180kd. [refseq;acc:nm_007366] Divided 205.102 205.132 1.00015
TRPC4 Rooted short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 70.7177 70.6355 1.00116
Subtracted 0.0822
5011 EXOC7 Measured exocyst complex component exo70. [swissprot;acc:q9upt5] Divided 7172.29 7168.41 1.00054
NEK1 Ranked serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] 205.104 205.135 1.00015
NFIL3 Squared nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] 45445.5 45433.1 1.00027
Subtracted 12.4
PLA2R1 Ranked phospholipase a2 receptor 1, 180kda; phospholipase a2 receptor 1, 180kd. [refseq;acc:nm_007366] 205.102 205.132 0.03
RBM5 Measured rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] 9412.17 9416.13 3.96
TBC1D10A Rooted ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Divided 70.7228 70.6584 1.00091
Subtracted 0.0644
5012 no value Ranked ganglioside induced differentiation associated protein 2; likely ortholog of mouse ganglioside-induced differentiation-associated-protein 2. [refseq;acc:nm_017686] Divided 192.907 192.879 1.00015
EXOC7 Measured exocyst complex component exo70. [swissprot;acc:q9upt5] Subtracted 7172.29 7168.41 3.88
LY75 Ranked lymphocyte antigen 75. [refseq;acc:nm_002349] 205.102 205.132 0.03
ODC1 Squared ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Divided 48085.3 48094.4 1.00019
Subtracted 9.1
RBM5 Measured rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] Divided 9412.17 9416.13 1.00042
TRPC5 Rooted short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 70.7228 70.6584 1.00091
Subtracted 0.0644
5013 ADC Squared ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] 48083.1 48090.5 7.4
AP2M1 Rooted clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] Divided 67.2652 67.2072 1.00086
LY75 Ranked lymphocyte antigen 75. [refseq;acc:nm_002349] 205.102 205.132 1.00015

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/