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 7308 to 7357 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
914 glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] Squared Subtracted 26914.1 30594.2 3680.1
guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] Ranked 237.558 229.677 7.881
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Measured 4997 5557.17 560.17
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Ranked Divided 210.863 218.878 1.03801
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Rooted Subtracted 62.4102 66.0829 3.6727
915 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Measured Divided 6289.72 6911.96 1.09893
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Rooted 55.2209 52.1262 1.05937
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Squared 19364.5 22408.8 1.15721
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Subtracted 17543.3 21222.5 3679.2
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Ranked Divided 146.036 140.692 1.03798
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Rooted Subtracted 62.4087 66.0813 3.6726
zinc finger protein t86. [swissprot;acc:o00488] Measured 4052.77 4612.54 559.77
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Ranked 237.558 229.677 7.881
916 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] Rooted Divided 61.4775 65.1209 1.05926
atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] Subtracted 62.4093 66.0819 3.6726
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Measured Divided 6289.72 6911.96 1.09893
fibulin-1 precursor. [swissprot;acc:p23142] Squared 44407.1 51387.4 1.15719
histone h4. [swissprot;acc:p02304] Ranked Subtracted 227.765 219.902 7.863
hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] Divided 232.512 241.288 1.03774
pescadillo homolog 1. [swissprot;acc:o00541] Measured Subtracted 3751.14 4310.89 559.75
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Squared 17543.3 21222.5 3679.2
917 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Ranked 86.7483 78.8995 7.8488
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Squared Divided 23294.5 26946.3 1.15677
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Measured 6289.72 6911.96 1.09893
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Squared Subtracted 14464.3 18142.8 3678.5
parafibromin. [refseq;acc:nm_024529] Ranked Divided 239.704 230.991 1.03772
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Measured Subtracted 5036.92 5596.36 559.44
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Rooted Divided 82.3879 87.2663 1.05921
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Subtracted 62.409 66.0815 3.6725
918 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] Divided 62.3496 66.0388 1.05917
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Ranked Subtracted 217.942 210.139 7.803
metastasis-associated protein mta1. [swissprot;acc:q13330] Squared Divided 23321.7 26976.4 1.15671
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Subtracted 14464.3 18142.8 3678.5
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Ranked Divided 212.952 205.292 1.03731
scratch; scratch 1. [refseq;acc:nm_031309] Measured 7281.6 8001.64 1.09888
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Subtracted 6288.27 6846.97 558.7
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Rooted 62.3617 66.0327 3.671
919 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Squared Divided 23346.9 27004.3 1.15665
cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Subtracted 31810.3 35473.9 3663.6
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Measured Divided 5396.36 5929.41 1.09878
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Ranked Subtracted 217.942 210.139 7.803
midasin (midas-containing protein). [swissprot;acc:q9nu22] Divided 237.218 228.698 1.03725
p66 alpha. [refseq;acc:nm_017660] Rooted 93.8375 88.6044 1.05906
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Measured Subtracted 6287.07 6845.28 558.21
920 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] Ranked 216.501 224.27 7.769
chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Squared 23346.9 27004.3 3657.4
deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] Ranked Divided 236.741 245.547 1.0372
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Measured 7273.78 7991.72 1.0987
protein cgi-147. [swissprot;acc:q9y3e5] Squared 36787.9 31806.3 1.15662

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/