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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2201 to 2250 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1101 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] Divided 6133.83 6690.18 1.0907
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Subtracted 6721.25 7238.34 517.09
1102 phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Divided 5462.88 5958.12 1.09066
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Subtracted 7433.73 7950.61 516.88
1103 ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Divided 5358.18 5843.73 1.09062
transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9] Subtracted 7433.73 7950.61 516.88
1104 kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Divided 5359.72 5844.97 1.09054
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Subtracted 7433.73 7950.61 516.88
1105 cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Divided 5460.49 5954.62 1.09049
1106 neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Subtracted 7433.73 7950.61 516.88
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] Divided 5489.99 5986.63 1.09046
1107 phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617]
transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] Subtracted 7433.73 7950.61 516.88
1108 nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494]
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Divided 4846.16 5283.08 1.09016
1109 nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] Subtracted 7433.73 7950.61 516.88
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Divided 6545.19 7132.89 1.08979
1110 mstp028 protein. [refseq;acc:nm_031954] Subtracted 5838.87 6355.06 516.19
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Divided 5947.53 6481.56 1.08979
1111 putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Subtracted 5393.37 5909.47 516.1
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Divided 6540.61 7127.41 1.08972
1112 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 5910.54 6440.58 1.08968
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Subtracted 5840.01 6355.56 515.55
1113 phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Divided 5910.54 6440.58 1.08968
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] Subtracted 5950.27 6465.72 515.45
1114 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] 6021.21 6536.45 515.24
phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259] Divided 5910.54 6440.58 1.08968
1115 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 5795.13 6314.19 1.08957
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Subtracted 5840.65 6355.84 515.19
1116 dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] Divided 5322.16 5798.38 1.08948
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Subtracted 5840.77 6355.89 515.12
1117 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Divided 5322.16 5798.38 1.08948
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Subtracted 6001.16 6515.9 514.74
1118 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] Divided 5322.16 5798.38 1.08948
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Subtracted 3658.76 3144.39 514.37
1119 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] Divided 5322.16 5798.38 1.08948
orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] Subtracted 6230.49 6744.5 514.01
1120 heat shock factor binding protein 1. [swissprot;acc:o75506] Divided 5915.42 6443.77 1.08932
nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] Subtracted 6230.38 6744.35 513.97
1121 nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Divided 4338.49 4725.86 1.08929
orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] Subtracted 6229.16 6742.79 513.63
1122 importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] 5792.08 6305.67 513.59
isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Divided 7937.72 8646.38 1.08928
1123 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 5857.48 6380.4 1.08927
interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Subtracted 5651.07 6164.55 513.48
1124 suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] 5946.33 6459.79 513.46
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Divided 6288.27 6846.97 1.08885
1125 glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] Subtracted 5946.33 6459.79 513.46
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Divided 6287.07 6845.28 1.08879

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/