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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 3408 to 3457 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
213 signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Squared Divided 1 86861.5 65369.7 1.32877
214 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Measured Subtracted 0 1217.92 1367.83 149.91
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Rooted 1 121.695 131.815 10.12
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked Divided 191.644 170.192 1.12605
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Measured Subtracted 7711.36 6265.79 1445.57
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Ranked 241.282 266.12 24.838
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Squared Divided 0 98.1677 70.141 1.39958
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Subtracted 1 28994.2 17134.8 11859.4
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Rooted 0 34.7164 32.0874 2.629
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Ranked Divided 7621.99 8473.85 1.11176
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Rooted 1 105.205 92.2415 1.14054
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Measured 0 13174.7 15605.1 1.18447
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Squared Subtracted 634.375 361.911 272.464
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Rooted Divided 21.5042 18.9231 1.1364
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Squared 1 52591.3 69845.1 1.32807
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Ranked Subtracted 0 14898.9 16041.6 1142.7
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Measured Divided 1 4074.83 5086.49 1.24827
215 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Subtracted 0 1658.23 1805.52 147.29
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Rooted Divided 1 105.205 92.2415 1.14054
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 0 9.36926 8.24639 1.13617
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked Subtracted 1 237.292 212.457 24.835
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Rooted 0 24.8155 27.4116 2.5961
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 1 121.695 131.815 10.12
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Ranked Divided 112 126 1.125
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Squared 0 98.1677 70.141 1.39958
myosin vi. [swissprot;acc:q9um54] Ranked 10121.5 11250.5 1.11154
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Measured Subtracted 1 7711.31 6265.76 1445.55
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 28994.2 17134.8 11859.4
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Divided 86609.4 65234.5 1.32766
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Subtracted 0 492.157 225.924 266.233
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Ranked 7955.61 6817.49 1138.12
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Measured Divided 1 16074 12888.4 1.24717
zinc finger protein 277. [swissprot;acc:q9nrm2] 0 13174.7 15605.1 1.18447
216 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 12478 14756 1.18256
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Rooted 9.36926 8.24639 1.13617
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Measured Subtracted 1658.07 1805.36 147.29
enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 1 10067.9 11511 1443.1
high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] Ranked 0 5677.96 4546.87 1131.09
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] Squared Divided 9.56237 6.91035 1.38378
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Rooted Subtracted 1 121.695 131.815 10.12
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Squared 46785.7 58383.2 11597.5
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Measured Divided 16071.6 12886.8 1.24714
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Ranked 0 10559.7 11732 1.11102
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 1 112 126 1.125
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Rooted 105.205 92.2415 1.14054
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] Squared Subtracted 0 492.157 225.924 266.233
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Divided 1 86600.9 65229.9 1.32763
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Ranked Subtracted 226.471 201.769 24.702
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Rooted 0 21.5042 18.9231 2.5811
217 40s ribosomal protein s29. [swissprot;acc:p30054] 26.1023 28.6733 2.571

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/