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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 3008 to 3057 of 3206 in total
Rank
description
measured
expected
final
Hugo
3008 SEPTIN 6. [SWISSPROT;Acc:Q14141] 0.116797 0.952641 0.122603373 SEPT6
3009 SEPTIN 7 (CDC10 PROTEIN HOMOLOG). [SWISSPROT;Acc:Q16181] 0.09144 0.749104 0.122065828 SEPT7
3010 BRAIN PROTEIN 44. [SWISSPROT;Acc:O95563] 0.0199967 0.163819 0.122065817 BRP44
3011 LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR (LYMPHOCYTE IGE RECEPTOR) (FC-EPSILON-RII) (CD23) (BLAST-2) (IMMUNOGLOBULIN E-BINDING FACTOR). [SWISSPROT;Acc:P06734] 0.0174686 0.14338 0.121834287 FCER2
3012 CD209 ANTIGEN; DENDRITIC CELL-SPECIFIC ICAM3-GRABBING NONINTEGRIN. [RefSeq;Acc:NM_021155] 0.0231389 0.189922 0.1218337 CD209
3013 0.0325023 0.266776 0.121833673 FRY
3014 SET DOMAIN AND MARINER TRANSPOSASE FUSION GENE. [RefSeq;Acc:NM_006515] 0.379831 3.11762 0.121833642 SETMAR
3015 CD209 ANTIGEN-LIKE; PUTATIVE TYPE II MEMBRANE PROTEIN. [RefSeq;Acc:NM_014257] 0.0247893 0.203469 0.121833301 CLEC4M
3016 COATOMER GAMMA SUBUNIT (GAMMA-COAT PROTEIN) (GAMMA-COP). [SWISSPROT;Acc:Q9Y678] 0.250617 2.06452 0.121392382 COPG
3017 COATOMER DELTA SUBUNIT (DELTA-COAT PROTEIN) (DELTA-COP) (ARCHAIN). [SWISSPROT;Acc:P48444] 0.293026 2.41388 0.121392116 ARCN1
3018 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E (EC 5.2.1.8) (PPIASE E) (ROTAMASE E) (CYCLOPHILIN E) (CYCLOPHILIN 33). [SWISSPROT;Acc:Q9UNP9] 0.0424091 0.349357 0.121391871 PPIE
3019 COATOMER ZETA-2 SUBUNIT (ZETA-2 COAT PROTEIN) (ZETA-2 COP). [SWISSPROT;Acc:Q9P299] 0.154284 1.27096 0.121391704 COPZ2
3020 COATOMER BETA' SUBUNIT (BETA'-COAT PROTEIN) (BETA'-COP) (P102). [SWISSPROT;Acc:P35606] 0.169636 1.39743 0.121391411 COPB2
3021 COATOMER ZETA-1 SUBUNIT (ZETA-1 COAT PROTEIN) (ZETA-1 COP) (CGI-120) (HSPC181). [SWISSPROT;Acc:Q9Y3C3] COPZ1
3022 SEPTIN 10 ISOFORM 1. [RefSeq;Acc:NM_144710] 0.106813 0.88182 0.121127895 SEPT10
3023 SEPTIN-LIKE PROTEIN KIAA0202 (FRAGMENT). [SWISSPROT;Acc:Q92599] 0.118014 0.986632 0.119612986 SEPT8
3024 SYNBINDIN (TRS23 HOMOLOG) (HEMATOPOIETIC STEM/PROGENITOR CELL PROTEIN 172) (HSPC172) (PTD009) (CGI-104). [SWISSPROT;Acc:Q9Y296] 0.0250043 0.209553 0.119322081 no value
3025 SEDLIN. [SWISSPROT;Acc:O14582] ZNF547
3026 BET3 HOMOLOG. [SWISSPROT;Acc:O43617] 0.125021 1.04777 0.119321034 TRAPPC3
3027 T-COMPLEX ASSOCIATED-TESTIS-EXPRESSED 1-LIKE (PROTEIN 91/23). [SWISSPROT;Acc:P51808] 0.0365656 0.307503 0.11891136 DYNLT3
3028 DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11A (MRE11 HOMOLOG 1). [SWISSPROT;Acc:P49959] 0.121552 1.02221 0.118910987 MRE11A
3029 COATOMER BETA SUBUNIT (BETA-COAT PROTEIN) (BETA-COP). [SWISSPROT;Acc:P53618] 0.329144 2.79482 0.117769302 COPB1
3030 UBIQUITIN-CONJUGATING ENZYME E2E 3; UBIQUITIN CARRIER PROTEIN; UBIQUITIN-PROTEIN LIGASE. [RefSeq;Acc:NM_006357] 0.167012 1.41955 0.117651368 UBE2E4P
3031 0.128895 1.09557 0.117651086 PTCD1
3032 0.191363 1.62653 0.117651073 UBE2E2
3033 UBIQUITIN-CONJUGATING ENZYME E2 E1 (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE E1) (UBIQUITIN CARRIER PROTEIN E1) (UBCH6). [SWISSPROT;Acc:P51965] 0.157204 1.33619 0.117650933 UBE2E1
3034 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] 0.146213 1.27404 0.114763273 no value
3035 TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P62 SUBUNIT (BASIC TRANSCRIPTION FACTOR 62 KDA SUBUNIT) (BTF2-P62) (GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 1). [SWISSPROT;Acc:P32780] 0.0306863 0.267389 0.114762761 GTF2H1
3036 GABA(A) RECEPTOR-ASSOCIATED PROTEIN; GABA(A)-RECEPTOR-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_007278] 0.125771 1.12068 0.112227398 GABARAP
3037 "PANTOTHENATE KINASE 2, MITOCHONDRIAL PRECURSOR (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 2) (HPANK2). [SWISSPROT;Acc:Q9BZ23]" 0.0193888 0.176603 0.109787489 PANK2
3038 PANTOTHENATE KINASE 1 (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 1) (HPANK1) (HPANK). [SWISSPROT;Acc:Q8TE04] 0.0241982 0.22041 0.109787215 PANK1
3039 "28S RIBOSOMAL PROTEIN S17, MITOCHONDRIAL PRECURSOR (MRP-S17) (HSPC011). [SWISSPROT;Acc:Q9Y2R5]" MRPS17
3040 PANTOTHENATE KINASE 3 (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 3) (HPANK3). [SWISSPROT;Acc:Q9H999] 0.0191226 0.174179 0.109787058 PANK3
3041 MITOCHONDRIAL SOLUTE CARRIER PROTEIN. [RefSeq;Acc:NM_145305] 0.0228794 0.208398 0.109787042 SLC25A43
3042 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-7 SUBUNIT. [SWISSPROT;Acc:O60262] 0.0391008 0.366305 0.106743834 no value
3043 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-12 SUBUNIT. [SWISSPROT;Acc:Q9UBI6] GNG12
3044 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-4 SUBUNIT. [SWISSPROT;Acc:P50150] 0.0328245 0.307647 0.106695336 GNG4
3045 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-3 SUBUNIT. [SWISSPROT;Acc:P29798] 0.0326969 0.306454 0.106694316 GNG3
3046 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-8 SUBUNIT (GAMMA-9). [SWISSPROT;Acc:Q9UK08] 0.032048 0.300389 0.106688327 GNG8
3047 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 SUBUNIT. [SWISSPROT;Acc:P30670] 0.0317927 0.298003 0.106685839 GNG5
3048 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-10 SUBUNIT. [SWISSPROT;Acc:P50151] 0.031665 0.29681 0.106684411 GNG10
3049 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. [SWISSPROT;Acc:Q9Y3K8] 0.0312821 0.293231 0.10668074 no value
3050 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-11 SUBUNIT. [SWISSPROT;Acc:P50152] 0.0293247 0.274937 0.106659707 GNG11
3051 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(T) BETA SUBUNIT 1 (TRANSDUCIN BETA CHAIN 1). [SWISSPROT;Acc:P04901] 0.204254 1.92471 0.106121961 GNB1
3052 "BASIC HELIX-LOOP-HELIX DOMAIN CONTAINING, CLASS B, 5; TRINUCLEOTIDE REPEAT CONTAINING 20. [RefSeq;Acc:NM_152414]" 0.090943 0.857352 0.106074285 BHLHB5
3053 BA305P22.3 (BREAST CARCINOMA AMPLIFIED SEQUENCE 4). [SPTREMBL;Acc:Q8NDY6] 0.0691801 0.65236 0.106045895 BHLHB4
3054 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Y), ALPHA SUBUNIT (ALPHA-11). [SWISSPROT;Acc:P29992]" 0.0392019 0.371714 0.105462533 GNA11
3055 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Q), ALPHA SUBUNIT. [SWISSPROT;Acc:P50148]" 0.0395834 0.375337 0.105460959 GNAQ
3056 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Z), ALPHA SUBUNIT (G(X) ALPHA CHAIN) (GZ-ALPHA). [SWISSPROT;Acc:P19086]" 0.0438075 0.415448 0.10544641 GNAZ
3057 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1 SUBUNIT (TRANSDUCIN ALPHA-1 CHAIN). [SWISSPROT;Acc:P11488]" 0.044407 0.421142 0.105444244 GNAT1

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/