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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Value Type Rank Interaction Map Gene Filtered description Network Comparison Type green red 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
Network Comparison Type
green
red
network_comparison
126 0 calcyphosine. [swissprot;acc:q13938] Divided 635.875 472.524 1.3457
pp3111 protein. [refseq;acc:nm_022156] Subtracted 530 789 259
1 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Divided 18164.9 24250 1.33499
rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted 2394.5 450.5 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] 1759.22 2017.91 258.69
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Divided 64 86 1.34375
1 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Subtracted 2394.5 450.5 1944
transcription factor jun-d. [swissprot;acc:p17535] Divided 7523.39 5638.2 1.33436
128 0 importin 9. [refseq;acc:nm_018085] Subtracted 1397.66 1143.55 254.11
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Divided 60.8613 81.504 1.33918
1 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 5810.82 4355.61 1.3341
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Subtracted 12944.2 11004.2 1940
129 0 nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] 1397.66 1143.55 254.11
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided 454.837 606.485 1.33341
1 luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 5811.49 4358.13 1.33348
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Subtracted 13346.9 15274.9 1928
130 0 chromodomain y-like protein 2. [refseq;acc:nm_152342] 2799.81 3053.31 253.5
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Divided 56 42 1.33333
1 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 2978.53 2234.68 1.33287
p66 alpha. [refseq;acc:nm_017660] Subtracted 10911.1 12839 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] 4658.69 4912.01 253.32
serpin b11. [swissprot;acc:q96p15] Divided 56 42 1.33333
1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 2978.57 2234.73 1.33285
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Subtracted 10911.1 12839 1927.9
132 0 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Divided 56 42 1.33333
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Subtracted 2202 1949.36 252.64
1 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Divided 2980.35 2236.61 1.33253
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Subtracted 10911.1 12839 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] Divided 335 252 1.32937
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Subtracted 2784.59 3036.85 252.26
1 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 10887.2 12798.9 1911.7
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Divided 17580.4 23421.5 1.33225
134 0 mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 346.751 260.986 1.32862
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Subtracted 2784.08 3036.29 252.21
1 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 10886 12796.8 1910.8
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided 16426.1 21785.2 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] Subtracted 476.619 728.65 252.031
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Divided 613.614 814.485 1.32736
1 apg3p; pc3-96 protein. [refseq;acc:nm_022488] 16426.1 21785.2 1.32626
transcription factor jun-b. [swissprot;acc:p17275] Subtracted 7488.4 5579.18 1909.22
136 0 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 1152.06 903.767 248.293
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Divided 1150.51 1526.38 1.3267
1 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Subtracted 10880.5 12787.6 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] Divided 4763.34 3620.77 1.31556
137 0 heat shock factor binding protein 1. [swissprot;acc:o75506] 1233.41 1631.18 1.3225
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Subtracted 7276.12 7520.78 244.66
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] Divided 4763.34 3620.77 1.31556
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Subtracted 10879.9 12786.6 1906.7
138 0 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 1906.28 1663.73 242.55
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] Divided 154.804 204.382 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/