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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 125 to 174 of 8289 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
63 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] High confidence 266.865 336.178 1.25973
RBM7 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Low confidence 265.688 239.902 1.10749
64 GNG11 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] High confidence 266.868 336.159 1.25965
JUND transcription factor jun-d. [swissprot;acc:p17535] Low confidence 202.709 183.361 1.10552
65 GNAQ guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] High confidence 267.136 336.077 1.25807
JUNB transcription factor jun-b. [swissprot;acc:p17275] Low confidence 202.728 183.388 1.10546
66 GNA11 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] High confidence 267.136 336.077 1.25807
MTUS1 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Low confidence 221.902 200.783 1.10518
67 GNAT2 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] High confidence 267.14 336.075 1.25805
UBR4 retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Low confidence 165.535 149.799 1.10505
68 no value 60s ribosomal protein l37a. [swissprot;acc:p12751] 239.692 217.005 1.10455
GNAZ guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] High confidence 267.139 336.075 1.25805
69 GNAT1 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 267.14
TEX28P2 testis-specific protein tex28. [swissprot;acc:o15482] Low confidence 259.517 235.017 1.10425
70 GNAI2 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] High confidence 267.142 336.074 1.25804
GOSR2 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] Low confidence 259.517 235.017 1.10425
71 no value cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] 230.944 209.149 1.10421
GNAI1 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] High confidence 267.144 336.073 1.25802
72 GNAI3 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]
SMYD2 set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Low confidence 230.944 209.149 1.10421
73 JPH3 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence 288 362 1.25694
SMYD1 set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Low confidence 230.944 209.149 1.10421
74 AHCYL1 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 195.817 215.516 1.1006
JPH2 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence 288 362 1.25694
75 GBAS nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] Low confidence 249.709 226.944 1.10031
SMPD2 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] High confidence 288 362 1.25694
76 NIPSNAP1 nipsnap1 protein. [swissprot;acc:q9bpw8] Low confidence 249.584 226.86 1.10017
TMEM33 db83 protein. [swissprot;acc:p57088] High confidence 288 362 1.25694
77 no value putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Low confidence 195.851 215.424 1.09994
CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] High confidence 254.692 202.668 1.2567
78 CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 254.693
LENG4 malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] Low confidence 211 231.635 1.0978
79 APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 229.144 208.803 1.09742
CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] High confidence 254.693 202.668 1.2567
80 CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 254.691 1.25669
RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] Low confidence 221.194 202.005 1.09499
81 CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] High confidence 254.614 202.646 1.25645
TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Low confidence 227.623 208.281 1.09286
82 DGKH diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] 226.981 208.077 1.09085
GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] High confidence 267.636 335.359 1.25304
83 DGKD diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Low confidence 226.981 208.077 1.09085
MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] High confidence 88.2482 110.265 1.24949
84 no value transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Low confidence 226.338 207.874 1.08882
MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] High confidence 88.2482 110.265 1.24949
85 no value melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Low confidence 225.735 245.308 1.08671
86 DFFB dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] 233.922 215.309 1.08645
MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] High confidence 88.2482 110.265 1.24949
87 KCND3 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Low confidence 225.545 244.933 1.08596
MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] High confidence 88.2482 110.265 1.24949

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/