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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Gene description Rank measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2158 to 2207 of 3206 in total
description
Rank
measured
expected
final
Hugo
MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P38 (JTV-1 PROTEIN) (PRO0992). [SWISSPROT;Acc:Q13155] 1929 0.122792 0.529927 0.231714934 no value
MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P43 [CONTAINS: ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II (EMAP-II) (SMALL INDUCIBLE CYTOKINE SUBFAMILY E MEMBER 1)]. [SWISSPROT;Acc:Q12904] 2803 0.388823 1.9597 0.19840945 SCYE1
MUSASHI 1. [RefSeq;Acc:NM_002442] 165 0.0416456 0.120995 0.344192735 MSI1
MUSASHI 2 ISOFORM A. [RefSeq;Acc:NM_138962] 164 0.0370125 0.107534 0.344193464 MSI2
MUSCLE-SPECIFIC BETA 1 INTEGRIN BINDING PROTEIN. [RefSeq;Acc:NM_014446] 2886 0.0771117 0.428402 0.179998459 ITGB1BP3
MY016 PROTEIN. [SPTREMBL;Acc:Q9H3K6] 2438 0.12244 0.563645 0.21722893 BOLA2B
MYB PROTO-ONCOGENE PROTEIN (C-MYB). [SWISSPROT;Acc:P10242] 1278 0.139096 0.564523 0.24639563 MYB
MYB-RELATED PROTEIN A (A-MYB). [SWISSPROT;Acc:P10243] 1359 0.106233 0.433454 0.24508483 MYBL1
MYB-RELATED PROTEIN B (B-MYB). [SWISSPROT;Acc:P10244] 1333 0.102811 0.419099 0.245314353 MYBL2
MYC PROTO-ONCOGENE PROTEIN (C-MYC). [SWISSPROT;Acc:P01106] 335 0.304036 1.06655 0.285064929 MYC
MYELIN GENE EXPRESSION FACTOR 2. [RefSeq;Acc:NM_016132] 1180 0.248404 0.996772 0.249208445 MYEF2
MYELIN P2 PROTEIN. [SWISSPROT;Acc:P02689] 288 0.0373888 0.123882 0.301809787 PMP2
MYO-INOSITOL 1-PHOSPHATE SYNTHASE A1. [RefSeq;Acc:NM_016368] 2441 0.0388043 0.178742 0.217096709 no value
MYOFIBRILLOGENESIS REGULATOR 1; TRANS-ACTIVATED BY HEPATITIS C VIRUS CORE PROTEIN 2; LIKELY ORTHOLOG OF MOUSE BRAIN PROTEIN 17. [RefSeq;Acc:NM_022572] 2587 0.48801 2.292 0.212918848 PNKD
MYOSIN VB (MYOSIN 5B) (FRAGMENT). [SWISSPROT;Acc:Q9ULV0] 3128 0.113029 1.65007 0.068499518 MYO5B
MYOSIN VC (MYOSIN 5C). [SWISSPROT;Acc:Q9NQX4] 3130 0.121984 1.78081 0.068499166 MYO5C
MYOSIN VI. [SWISSPROT;Acc:Q9UM54] 1646 0.050323 0.210535 0.23902439 no value
MYOSIN VIIA. [SWISSPROT;Acc:Q13402] 1395 0.066057 0.270441 0.244256603 MYO7A
MYOSIN XV (UNCONVENTIONAL MYOSIN-15). [SWISSPROT;Acc:Q9UKN7] 526 0.0249116 0.0916194 0.271903112 MYO15A
N-ACETYLGALACTOSAMINE KINASE (EC 2.7.1.-) (GALNAC KINASE) (GALACTOKINASE 2). [SWISSPROT;Acc:Q01415] 2676 0.0435693 0.20874 0.208725208 GALK2
N-ACETYLGLUTAMATE SYNTHASE. [RefSeq;Acc:NM_153006] 2073 0.517899 2.25773 0.229389254 NAGS
N-ACETYLTRANSFERASE 5 (EC 2.3.1.-). [SWISSPROT;Acc:Q9Y6D2] 1833 0.101148 0.43244 0.233900657 NAT5
N-DEACETYLASE/N-SULFOTRANSFERASE (HEPARAN GLUCOSAMINYL) 3. [RefSeq;Acc:NM_004784] 2204 0.0316607 0.140415 0.225479472 NDST3
N-DEACETYLASE/N-SULFOTRANSFERASE 4. [RefSeq;Acc:NM_022569] 2205 0.0319117 0.141529 0.225478171 NDST4
N-MYC PROTO-ONCOGENE PROTEIN. [SWISSPROT;Acc:P04198] 330 0.238906 0.837663 0.285205387 MYCN
N-TERMINAL ACETYLTRANSFERASE COMPLEX ARD1 SUBUNIT HOMOLOG (EC 2.3.1.-). [SWISSPROT;Acc:P41227] 1291 0.304267 1.23733 0.245906104 ARD1A
NADH-CYTOCHROME B5 REDUCTASE (EC 1.6.2.2) (B5R). [SWISSPROT;Acc:P00387] 2201 0.0966308 0.427993 0.22577659 CYB5R3
NADH-UBIQUINONE OXIDOREDUCTASE B14 SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-B14) (CI-B14). [SWISSPROT;Acc:P56556] 146 0.0694539 0.197664 0.351373543 NDUFA6
NADH-UBIQUINONE OXIDOREDUCTASE B22 SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-B22) (CI-B22). [SWISSPROT;Acc:Q9Y6M9] 271 0.201492 0.658159 0.306144868 NDUFB9
NADH-UBIQUINONE OXIDOREDUCTASE PDSW SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-PDSW) (CI-PDSW). [SWISSPROT;Acc:O96000] 1533 0.322293 1.3313 0.242088936 NDUFB10
NADH-UBIQUINONE OXIDOREDUCTASE SUBUNIT B17.2 (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-B17.2) (CI-B17.2) (CIB17.2) (13 KDA DIFFERENTIATION-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9UI09] 2721 0.0767473 0.371275 0.206712814 NDUFA12
NADPH-CYTOCHROME P450 REDUCTASE (EC 1.6.2.4) (CPR) (P450R). [SWISSPROT;Acc:P16435] 1917 0.0187206 0.0807026 0.231970222 POR
NAG14 PROTEIN. [RefSeq;Acc:NM_022143] 541 0.0376313 0.138821 0.271077863 LRRC4
NARDILYSIN PRECURSOR (EC 3.4.24.61) (N-ARGININE DIBASIC CONVERTASE) (NRD CONVERTASE) (NRD-C). [SWISSPROT;Acc:O43847] 726 0.0787172 0.297409 0.26467659 NRD1
NASCENT-POLYPEPTIDE-ASSOCIATED COMPLEX ALPHA POLYPEPTIDE. [RefSeq;Acc:NM_005594] 249 0.804734 2.57998 0.311914821 no value
NECDIN. [SWISSPROT;Acc:Q99608] 3153 0.0654743 1.00142 0.065381458 NDN
NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [RefSeq;Acc:NM_024946] 1567 0.0394801 0.163824 0.240990941 no value
NEIGHBOR OF COX4. [SWISSPROT;Acc:O43402] 769 0.0269837 0.102351 0.263638851 COX4NB
NEMO-LIKE KINASE; LIKELY ORTHOLOG OF MOUSE NEMO LIKE KINASE. [RefSeq;Acc:NM_016231] 1701 0.210207 0.883788 0.237847764 NLK
NEURAL CELL ADHESION MOLECULE L1 PRECURSOR (N-CAM L1) (CD171 ANTIGEN). [SWISSPROT;Acc:P32004] 2666 0.02527 0.120774 0.209233775 no value
NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN (N-WASP). [SWISSPROT;Acc:O00401] 43 1.66627 3.96399 0.420351716 WASL
NEURALIZED-LIKE. [RefSeq;Acc:NM_004210] 158 0.096416 0.274876 0.350761798 NEURL
NEUROCALCIN DELTA. [SWISSPROT;Acc:P29554] 1225 0.14688 0.592229 0.248012171 NCALD
NEUROENDOCRINE DIFFERENTIATION FACTOR; COMPARATIVE GENE IDENTIFICATION TRANSCRIPT 149. [RefSeq;Acc:NM_016079] 3197 0.027115 0.735578 0.036862168 VPS24
NEUROEPITHELIAL CELL TRANSFORMING GENE 1; GUANINE NUCLEOTIDE REGULATORY PROTEIN (ONCOGENE); RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 8. [RefSeq;Acc:NM_005863] 1528 0.0256013 0.105652 0.24231723 NET1
NEUROGENIC DIFFERENTIATION FACTOR 1 (NEUROD1) (NEUROD). [SWISSPROT;Acc:Q13562] 3102 0.0752577 0.816035 0.092223618 NEUROD1
NEUROGENIC DIFFERENTIATION FACTOR 2 (NEUROD2). [SWISSPROT;Acc:Q15784] 3103 0.0917931 0.995332 0.0922236 NEUROD2
NEUROGENIC DIFFERENTIATION FACTOR 4 (NEUROD4). [SWISSPROT;Acc:Q9HD90] 3106 0.0728267 0.789676 0.09222352 NEUROD4
NEUROGENIC DIFFERENTIATION FACTOR 6 (NEUROD6) (MY051 PROTEIN). [SWISSPROT;Acc:Q96NK8] 3105 0.0744473 0.807248 0.092223579 NEUROD6
NEURON NAVIGATOR 1; NEURON NAVIGATOR-1; PORE MEMBRANE AND/OR FILAMENT INTERACTING LIKE PROTEIN 3. [RefSeq;Acc:NM_020443] 20 0.149206 0.314027 0.475137488 NAV1

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
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/