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 expected description final measured Hugo
Results: HTML CSV LaTeX Showing element 3158 to 3206 of 3206 in total
Rank
expected
description
final
measured
Hugo
3158 1.14583 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 1 (MYOSIN HEAVY CHAIN IIX/D) (MYHC-IIX/D). [SWISSPROT;Acc:P12882]" 0.064710559 0.0741473 MYH1
3159 1.13857 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, PERINATAL (MYHC-PERINATAL). [SWISSPROT;Acc:P13535]" 0.064710558 0.0736775 MYH8
3160 1.05366 DJ756N5.1.1 (CONTINUES IN EM:AL133324 AS DJ1161H23.3) (FRAGMENT). [SPTREMBL;Acc:Q9H430] 0.064710438 0.0681828 MYH7B
3161 1.11332 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, EXTRAOCULAR (MYHC-EO). [SWISSPROT;Acc:Q9UKX3]" 0.064710416 0.0720434 MYH13
3162 1.125 "MYOSIN HEAVY CHAIN, FAST SKELETAL MUSCLE, EMBRYONIC (MUSCLE EMBRYONIC MYOSIN HEAVY CHAIN) (SMHCE). [SWISSPROT;Acc:P11055]" 0.0647104 0.0727992 MYH3
3163 1.26168 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE BETA ISOFORM (MYHC-BETA). [SWISSPROT;Acc:P12883]" 0.064710307 0.0816437 no value
3164 1.14331 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 2 (MYOSIN HEAVY CHAIN IIA) (MYHC-IIA). [SWISSPROT;Acc:Q9UKX2]" 0.064710271 0.0739839 MYH2
3165 1.13826 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, FETAL (MYOSIN HEAVY CHAIN IIB) (MYHC-IIB). [SWISSPROT;Acc:Q9Y623]" 0.06471026 0.0736571 MYH4
3166 1.26263 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE ALPHA ISOFORM (MYHC-ALPHA). [SWISSPROT;Acc:P13533]" 0.064710168 0.081705 no value
3167 11.3823 0.06471012 0.73655 C5orf33
3168 0.812069 "RIBOSOMAL PROTEIN S6 KINASE, 52KDA, POLYPEPTIDE 1; RIBOSOMAL PROTEIN S6 KINASE, 52KD, POLYPEPTIDE 1. [RefSeq;Acc:NM_012424]" 0.062788507 0.0509886 RPS6KC1
3169 0.619812 RIBOSOMAL PROTEIN S6 KINASE-LIKE 1. [RefSeq;Acc:NM_031464] 0.062788394 0.038917 no value
3170 0.485319 "T-COMPLEX PROTEIN 1, GAMMA SUBUNIT (TCP-1-GAMMA) (CCT-GAMMA). [SWISSPROT;Acc:P49368]" 0.059152434 0.0287078 CCT3
3171 0.74486 PROLINE SYNTHETASE CO-TRANSCRIBED BACTERIAL HOMOLOG PROTEIN. [SWISSPROT;Acc:O94903] 0.05906224 0.0439931 PROSC
3172 1.03955 NUCLEAR RNA EXPORT FACTOR 1 (TIP ASSOCIATING PROTEIN) (TIP-ASSOCIATED PROTEIN) (MRNA EXPORT FACTOR TAP). [SWISSPROT;Acc:Q9UBU9] 0.055582704 0.057781 NXF1
3173 0.846512 NUCLEAR RNA EXPORT FACTOR 3 (TAP-LIKE PROTEIN 3) (TAPL-3). [SWISSPROT;Acc:Q9H4D5] 0.055483206 0.0469672 NXF3
3174 0.820367 NUCLEAR RNA EXPORT FACTOR 5 (TAP-LIKE PROTEIN 1) (TAPL-1). [SWISSPROT;Acc:Q9H1B4] 0.055466395 0.0455028 NXF5
3175 0.333333 0.055311655 0.0184372 NIPA2
3176 C6orf130
3177 PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED; PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED PROTEIN. [RefSeq;Acc:NM_016172] UBAC1
3178 2.91316 S-PHASE KINASE-ASSOCIATED PROTEIN 1A (CYCLIN A/CDK2-ASSOCIATED PROTEIN P19) (P19A) (P19SKP1) (RNA POLYMERASE II ELONGATION FACTOR-LIKE PROTEIN) (ORGAN OF CORTI PROTEIN 2) (OCP-II PROTEIN) (OCP-2) (TRANSCRIPTION ELONGATION FACTOR B) (SIII). [SWISSPR 0.049776531 0.145007 SKP1A
3179 0.629022 CULLIN HOMOLOG 1 (CUL-1). [SWISSPROT;Acc:Q13616] 0.049776478 0.0313105 CUL1
3180 PRESENILIN 1 (PS-1) (S182 PROTEIN). [SWISSPROT;Acc:P49768] PSEN1
3181 0.486077 CULLIN HOMOLOG 2 (CUL-2). [SWISSPROT;Acc:Q13617] 0.049776476 0.0241952 CUL2
3182 1.77573 "F-BOX PROTEIN FBW7 ISOFORM 2; ARCHIPELAGO, DROSOPHILA, HOMOLOG OF; F-BOX PROTEIN FBW7; F-BOX PROTEIN SEL-10; HOMOLOG OF C ELEGANS SEL-10. [RefSeq;Acc:NM_018315]" 0.04977643 0.0883895 FBXW7
3183 0.517685 PRESENILIN 2 (PS-2) (STM-2) (E5-1) (AD3LP) (AD5). [SWISSPROT;Acc:P49810] 0.049776408 0.0257685 PSEN2
3184 1.32794 0.049410892 0.0656147 PYCRL
3185 1.01816 0.04678744 0.0476371 CCDC104
3186 0.834222 FICOLIN 2 PRECURSOR (COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2) (FICOLIN-B) (FICOLIN B) (SERUM LECTIN P35) (EBP-37) (HUCOLIN) (L- FICOLIN). [SWISSPROT;Acc:Q15485] 0.037315127 0.0311291 FCN2
3187 0.772261 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14C; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-81; PKC-POTENTIATED PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_030949]" 0.037315105 0.028817 no value
3188 0.648338 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14A; 17-KDA PKC-POTENTIATED INHIBITORY PROTEIN OF PP1. [RefSeq;Acc:NM_033256]" 0.037315104 0.0241928 PPP1R14A
3189 0.853372 MICROFIBRIL-ASSOCIATED GLYCOPROTEIN 4 PRECURSOR. [SWISSPROT;Acc:P55083] 0.037315028 0.0318436 MFAP4
3190 0.615511 "PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 14D; PKC-DEPENDENT PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_017726]" 0.037315011 0.0229678 PPP1R14D
3191 1.34852 0.037314982 0.05032 FIBCD1
3192 0.387764 ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM (AMSH) LIKE PROTEIN. [RefSeq;Acc:NM_020799] 0.03686237 0.0142939 STAMBPL1
3193 0.620827 PROTEIN HSPC134 (PROTEIN CDA04). [SWISSPROT;Acc:Q9BY43] 0.036862282 0.0228851 CHMP4A
3194 0.649583 0.036862264 0.0239451 CHMP4C
3195 0.486357 ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM. [RefSeq;Acc:NM_006463] 0.036862223 0.0179282 STAMBP
3196 0.85608 0.036862209 0.031557 CHMP4B
3197 0.735578 NEUROENDOCRINE DIFFERENTIATION FACTOR; COMPARATIVE GENE IDENTIFICATION TRANSCRIPT 149. [RefSeq;Acc:NM_016079] 0.036862168 0.027115 VPS24
3198 0.273869 PUTATIVE BREAST ADENOCARCINOMA MARKER (32KD). [RefSeq;Acc:NM_014453] 0.036862149 0.0100954 CHMP2A
3199 0.104721 0.036862138 0.00386024 CHMP2B
3200 1.63989 RAS-RELATED GTP BINDING A; RAS-RELATED GTP-BINDING PROTEIN. [RefSeq;Acc:NM_006570] 0.023892334 0.0391808 RRAGA
3201 1.21378 RAS-RELATED GTP BINDING C; RAG C PROTEIN. [RefSeq;Acc:NM_022157] 0.023892303 0.029 RRAGC
3202 1.20992 "ANILLIN, ACTIN BINDING PROTEIN (SCRAPS HOMOLOG, DROSOPHILA); ANILLIN (DROSOPHILA SCRAPS HOMOLOG), ACTIN BINDING PROTEIN. [RefSeq;Acc:NM_018685]" 0.023892241 0.0289077 ANLN
3203 1.78381 RAS-RELATED GTP BINDING B SHORT ISOFORM; GTP-BINDING PROTEIN RAGB. [RefSeq;Acc:NM_006064] 0.023892231 0.0426192 RRAGB
3204 0.81025 ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [RefSeq;Acc:NM_015915] 0.000219977 0.000178236 no value
3205 2.59675 0.000219976 0.000571223 C1orf166
3206 0.7865 0.000173011 no value

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/