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 Rank measured description Hugo expected final
Results: HTML CSV LaTeX Showing element 3058 to 3107 of 3206 in total
Rank
measured
description
Hugo
expected
final
3058 0.0446932 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-2 SUBUNIT (TRANSDUCIN ALPHA-2 CHAIN). [SWISSPROT;Acc:P19087]" GNAT2 0.423859 0.105443556
3059 0.0485629 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-2 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04899]" GNAI2 0.460606 0.105432626
3060 0.0510974 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT (ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN). [SWISSPROT;Acc:P04898]" GNAI1 0.484673 0.105426545
3061 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(K), ALPHA SUBUNIT (G(I) ALPHA-3). [SWISSPROT;Acc:P08754]" GNAI3
3062 0.204288 "T-COMPLEX PROTEIN 1, EPSILON SUBUNIT (TCP-1-EPSILON) (CCT-EPSILON). [SWISSPROT;Acc:P48643]" CCT5 1.93831 0.105394906
3063 0.18745 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT 4 (TRANSDUCIN BETA CHAIN 4). [SWISSPROT;Acc:Q9HAV0] GNB4 1.78008 0.105304256
3064 0.126175 CYSTEINE ENDOPEPTIDASE AUT-LIKE ISOFORM B. [RefSeq;Acc:NM_178326] ATG4B 1.21767 0.103620028
3065 0.0764589 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3A (MAP1A/MAP1B LC3 A) (MAP1A/1B LIGHT CHAIN 3 A). [SWISSPROT;Acc:Q9H492] MAP1LC3A 0.738297 0.103561168
3066 0.0670742 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B (MAP1A/MAP1B LC3 B) (MAP1A/1B LIGHT CHAIN 3 B). [SWISSPROT;Acc:Q9GZQ8] MAP1LC3B 0.647682 0.103560389
3067 0.156084 CYSTEINE ENDOPEPTIDASE AUT-LIKE 2 ISOFORM A; AUTOPHAGY-RELATED CYSTEINE ENDOPEPTIDASE 2; AUTOPHAGIN 2. [RefSeq;Acc:NM_052936] ATG4A 1.50787 0.103512902
3068 0.167175 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT 5 (TRANSDUCIN BETA CHAIN 5). [SWISSPROT;Acc:O14775] GNB5 1.61983 0.103205275
3069 0.0533885 no value 0.517345 0.103197093
3070 0.0365299 C1orf156 0.353982 0.103197055
3071 0.164494 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 4. [RefSeq;Acc:NM_030627] CPEB4 1.59398 0.103197029
3072 0.0659913 DAB2 INTERACTING PROTEIN; NGAP-LIKE PROTEIN; DOC-2/DAB2 INTERACTIVE PROTEIN. [RefSeq;Acc:NM_032552] DAB2IP 0.639469 0.103197028
3073 0.0550688 RAS GTPASE-ACTIVATING PROTEIN NGAP (RAS PROTEIN ACTIVATOR LIKE 1). [SWISSPROT;Acc:Q9UJF2] RASAL2 0.533628 0.103196984
3074 0.129151 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 3. [RefSeq;Acc:NM_014912] CPEB3 1.2515 0.103196964
3075 0.083343 TOB2 PROTEIN (TRANSDUCER OF ERBB-2 2). [SWISSPROT;Acc:Q14106] TOB2 0.807611 0.10319696
3076 0.102521 TOB1 PROTEIN (TRANSDUCER OF ERBB-2 1). [SWISSPROT;Acc:P50616] TOB1 0.993451 0.103196836
3077 0.13205 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 3. [RefSeq;Acc:NM_004838]" HOMER3 1.3211 0.099954583
3078 0.137954 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 1B. [RefSeq;Acc:NM_004272]" HOMER1 1.38037 0.099939871
3079 0.0444208 PLASMA CARBOXYPEPTIDASE B2 ISOFORM A PREPROPROTEIN; CARBOXYPEPTIDASE U; THROMBIN-ACTIVATABLE FIBRINOLYSIS INHIBITOR; CARBOXYPEPTIDASE B-LIKE PROTEIN; THROMBIN-ACTIVABLE FIBRINOLYSIS INHIBITOR. [RefSeq;Acc:NM_001872] CPB2 0.444481 0.09993858
3080 0.0451789 MAST CELL CARBOXYPEPTIDASE A PRECURSOR (EC 3.4.17.1) (MC-CPA) (CARBOXYPEPTIDASE A3). [SWISSPROT;Acc:P15088] CPA3 0.452071 0.09993762
3081 0.0454705 CARBOXYPEPTIDASE B PRECURSOR. [RefSeq;Acc:NM_020361] CPA6 0.454991 0.099937142
3082 0.0558136 UBIQUINONE BIOSYNTHESIS PROTEIN COQ7 HOMOLOG (COENZYME Q BIOSYNTHESIS PROTEIN 7 HOMOLOG) (TIMING PROTEIN CLK-1 HOMOLOG). [SWISSPROT;Acc:Q99807] COQ7 0.558604 0.09991622
3083 0.174683 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 2; HOMER HOMOLOG 3 (DROSOPHILA). [RefSeq;Acc:NM_004839]" HOMER2 1.74914 0.099867935
3084 0.0979655 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(T) BETA SUBUNIT 3 (TRANSDUCIN BETA CHAIN 3). [SWISSPROT;Acc:P16520] GNB3 0.982529 0.09970749
3085 0.0586001 DEOXYRIBONUCLEASE II BETA ISOFORM 1 PRECURSOR; DEOXYRIBONUCLEASE II BETA; ENDONUCLEASE DLAD. [RefSeq;Acc:NM_021233] DNASE2B 0.589168 0.099462462
3086 0.0398596 PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 5 PRECURSOR (EC 3.4.21.-) (PROPROTEIN CONVERTASE PC5) (SUBTILISIN/KEXIN-LIKE PROTEASE PC5) (CONVERTASE PC5) (PC6) (HPC6). [SWISSPROT;Acc:Q92824] PCSK5 0.408247 0.09763599
3087 0.038802 FAM20A 0.397415 0.097635972
3088 0.587123 CYTOPLASMIC DYNEIN LIGHT CHAIN (T-COMPLEX TESTIS-SPECIFIC PROTEIN 1 HOMOLOG) (PROTEIN CW-1). [SWISSPROT;Acc:Q15763] DYNLT1 6.01339 0.097635942
3089 0.048624 TM4SF19 0.498014 0.097635809
3090 METHYLTRANSFERASE LIKE 2. [RefSeq;Acc:NM_018396] no value
3091 METTL2A
3092 FZR1 PROTEIN; FIZZY-RELATED PROTEIN; CDC20-LIKE 1B. [RefSeq;Acc:NM_016263] FZR1
3093 0.0760798 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-5 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-5 SUBUNIT). [SWISSPROT;Acc:Q9UF02] CACNG5 0.782104 0.09727581
3094 0.0573556 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-4 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-4 SUBUNIT). [SWISSPROT;Acc:Q9UBN1] CACNG4 0.590154 0.097187514
3095 0.0571433 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-2 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-2 SUBUNIT). [SWISSPROT;Acc:Q9Y698] CACNG2 0.587978 0.097186119
3096 0.0570584 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-8 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-8 SUBUNIT). [SWISSPROT;Acc:Q8WXS5] CACNG8 0.587107 0.097185692
3097 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-3 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-3 SUBUNIT). [SWISSPROT;Acc:O60359] CACNG3
3098 0.112123 CG9578-LIKE; YEAST YPR037W AND WORM C02C2.6 PREDICTED PROTEINS-LIKE. [RefSeq;Acc:NM_152902] TIPRL 1.18537 0.094589031
3099 0.063706 "T-COMPLEX PROTEIN 1, ALPHA SUBUNIT (TCP-1-ALPHA) (CCT-ALPHA). [SWISSPROT;Acc:P17987]" TCP1 0.673766 0.094552115
3100 0.0506529 DGCR14 PROTEIN (DIGEORGE SYNDROME CRITICAL REGION 14) (ES2 PROTEIN). [SWISSPROT;Acc:Q96DF8] DGCR14 0.544557 0.093016709
3101 0.247158 DOC-1 RELATED PROTEIN (DOC-1R). [SWISSPROT;Acc:O75956] CDK2AP2 2.67998 0.092223823
3102 0.0752577 NEUROGENIC DIFFERENTIATION FACTOR 1 (NEUROD1) (NEUROD). [SWISSPROT;Acc:Q13562] NEUROD1 0.816035 0.092223618
3103 0.0917931 NEUROGENIC DIFFERENTIATION FACTOR 2 (NEUROD2). [SWISSPROT;Acc:Q15784] NEUROD2 0.995332 0.0922236
3104 0.0749538 CHROMODOMAIN HELICASE-DNA-BINDING PROTEIN 3 (CHD-3) (MI-2 AUTOANTIGEN 240 KDA PROTEIN) (MI2-ALPHA). [SWISSPROT;Acc:Q12873] CHD3 0.81274 0.092223589
3105 0.0744473 NEUROGENIC DIFFERENTIATION FACTOR 6 (NEUROD6) (MY051 PROTEIN). [SWISSPROT;Acc:Q96NK8] NEUROD6 0.807248 0.092223579
3106 0.0728267 NEUROGENIC DIFFERENTIATION FACTOR 4 (NEUROD4). [SWISSPROT;Acc:Q9HD90] NEUROD4 0.789676 0.09222352
3107 0.0762705 CHROMODOMAIN HELICASE DNA BINDING PROTEIN 5. [RefSeq;Acc:NM_015557] CHD5 0.827018 0.092223507

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/