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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Gene Value Type Rank Interaction Map Filtered description red green Network Comparison Type network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
Filtered
description
red
green
Network Comparison Type
network_comparison
126 0 calcyphosine. [swissprot;acc:q13938] 472.524 635.875 Divided 1.3457
pp3111 protein. [refseq;acc:nm_022156] 789 530 Subtracted 259
1 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 24250 18164.9 Divided 1.33499
rad50-interacting protein 1. [refseq;acc:nm_021930] 450.5 2394.5 Subtracted 1944
127 0 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 2017.91 1759.22 258.69
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 86 64 Divided 1.34375
1 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 450.5 2394.5 Subtracted 1944
transcription factor jun-d. [swissprot;acc:p17535] 5638.2 7523.39 Divided 1.33436
128 0 importin 9. [refseq;acc:nm_018085] 1143.55 1397.66 Subtracted 254.11
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 81.504 60.8613 Divided 1.33918
1 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 4355.61 5810.82 1.3341
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 11004.2 12944.2 Subtracted 1940
129 0 nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] 1143.55 1397.66 254.11
protein hspc134 (protein cda04). [swissprot;acc:q9by43] 606.485 454.837 Divided 1.33341
1 luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 4358.13 5811.49 1.33348
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 15274.9 13346.9 Subtracted 1928
130 0 chromodomain y-like protein 2. [refseq;acc:nm_152342] 3053.31 2799.81 253.5
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 42 56 Divided 1.33333
1 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 2234.68 2978.53 1.33287
p66 alpha. [refseq;acc:nm_017660] 12839 10911.1 Subtracted 1927.9
131 0 protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] 4912.01 4658.69 253.32
serpin b11. [swissprot;acc:q96p15] 42 56 Divided 1.33333
1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 2234.73 2978.57 1.33285
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 12839 10911.1 Subtracted 1927.9
132 0 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 42 56 Divided 1.33333
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 1949.36 2202 Subtracted 252.64
1 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 2236.61 2980.35 Divided 1.33253
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 12839 10911.1 Subtracted 1927.9
133 0 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 252 335 Divided 1.32937
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] 3036.85 2784.59 Subtracted 252.26
1 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 12798.9 10887.2 1911.7
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 23421.5 17580.4 Divided 1.33225
134 0 mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 260.986 346.751 1.32862
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 3036.29 2784.08 Subtracted 252.21
1 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 12796.8 10886 1910.8
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 21785.2 16426.1 Divided 1.32626
135 0 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 728.65 476.619 Subtracted 252.031
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] 814.485 613.614 Divided 1.32736
1 apg3p; pc3-96 protein. [refseq;acc:nm_022488] 21785.2 16426.1 1.32626
transcription factor jun-b. [swissprot;acc:p17275] 5579.18 7488.4 Subtracted 1909.22
136 0 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 903.767 1152.06 248.293
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 1526.38 1150.51 Divided 1.3267
1 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 12787.6 10880.5 Subtracted 1907.1
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 3620.77 4763.34 Divided 1.31556
137 0 heat shock factor binding protein 1. [swissprot;acc:o75506] 1631.18 1233.41 1.3225
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 7520.78 7276.12 Subtracted 244.66
1 ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 3620.77 4763.34 Divided 1.31556
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 12786.6 10879.9 Subtracted 1906.7
138 0 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 1663.73 1906.28 242.55
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] 204.382 154.804 Divided 1.32026

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/